Community Science Program: FY22 Proposal
Proposer’s Name: Olivier VALLON
Proposal Title: The Chlamydomonas pan-genome
Proposal (WIP) ID: 508098
Lay description: The land plants that make up our forests and produce most of our food have tiny relatives, called green algae. Their study allows us to learn more on how plants carry out photosynthesis, the only way nature can withdraw CO2 from the atmosphere, to build living matter. Among these inconspicuous organism, the unicellular Chlamydomonas reinhardtii is a key model organism, because of its ease of manipulation. It has been used in laboratories since 1945 and has allowed many discoveries. Our project will explore the natural biodiversity of this species and discover new functions for its many genes.
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A) Brief description:
Abstract: Chlamydomonas reinhardtii, with its 111 Mb genome, is the premier green algal model for research on photosynthesis, organelle biogenesis, lipid metabolism and for testing / designing biotechnology applications. It also serves as a model in research on cilia, the eukaryotic cell cycle, microbial interactions, nutrient homeostasis and other fields. Thanks to continuous efforts from the JGI, a genome has been available for a reference strain since the early 2000s, and the organism represents one of several flagship species for the JGI. Chlamydomonas reinhardtii is cosmopolitan, and next-gen sequencing of field isolates has revealed a surprisingly high genetic diversity, with SNP- level difference between strains of the same species as high as 3% and associated with a high phenotypic variability. We will harness the power of comparative genomics for a functional description of the genome features in this important model organism. We will sequence and assemble the genomes of up to 20 strains, most of them field isolates that either are available in collections or will be collected by us from the wild. This project is connected to a genome-wide association study using the "MAGIC" design that has already generated a large population of recombinant strains. The Chlamydomonas pan-genome not only will facilitate data analysis for individual investigator-initiated projects that rely on Chlamydomonas, but it will also help us understand how species- level diversity operates in natural environments to shape the phototrophic biome.
Scope of Work: Phase I, to start immediately, will consist in assembly and annotation of 10 strains, mostly field isolates, and annotation of 5 previously obtained chromosome-level assemblies. The core sequencing technology will be PacBio HiFi, run by JGI using DNA samples prepared by us, with possible contributions of HiC (JGI) for synteny analysis and scaffolding and/or Nanopore (external) for DNA methylation. Assembly will benefit from additional RNA-Seq or Iso-Seq data, generated by JGI. In Phase II, the consortium will isolate new wild strains from a diversity of locations worldwide. Using Illumina sequencing, we will select 10 novel strains presenting additional diversity, for JGI to assemble and annotate. All data will be analyzed by the consortium for synteny and orthology relationships, and eventually presented to the public in the form of a Chlamydomonas pan-genome database. All the PIs involved have contributed to Chlamydomonas genomics in multiple diverse ways, usually in close collaboration with JGI staff. While Illumina sequencing is appropriate to monitor genetic diversity, the level of divergence we observe is so high that genome assembly and structural annotation are necessary to correlate genotype and phenotype at the resolution of interest. Today, only JGI has the expertise and experience necessary for such an ambitious project involving up to 20 strains, both for assembly and structural annotation. Over the years, JGI has accumulated transcriptomic data and tools that allows its staff to generate a precise description of the transcripts, including alternatively-spliced isoforms, in a controlled pipeline that allows direct comparison between strains. We also rely on JGI's powerful functional annotation pipeline to generate deep homology-based insight into gene function.
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B) Background information:
Technical Information: The nuclear genome of Chlamydomonas, based on previous assemblies, is approximately 111 Mb in size, with a GC content of 64% (Merchant et al., 2007). It is composed of 17 chromosomes, ranging from 3.7 Mb to 9.8 Mb. A total of 269 transposable elements has been described in Chlamydomonas, which together account for 10.8-12.4% of the genome depending on the strain (Craig et al., 2021). Their diversity is high, with 8 of the 9 known TE orders represented, in 16 superfamilies. The high similarity between copies of the same TE (80% of copies exhibit <5% divergence from their consensus) explains some of the problems with assemblies generated before long reads were available. As a unicellular alga, Chlamydomonas is amenable to many microbiological techniques (Harris, 2009). In particular, large clonal cultures can be generated from a single cell in a matter of days. As a result, very little heterogeneity is expected in DNA preparations. Being haploid, the strains under study will not need haplotype phasing. Established protocols exist for preparation of high-quality DNA, that have been previously applied by us (Lin et al., 2013). They have allowed generation of highly contiguous assemblies after PacBio sequencing, some enjoying N50 values approaching 3 Mb.
Available Resources: The co-PIs of this proposal lead some of the most prominent laboratories working on Chlamydomonas. Accordingly, they have significant financial support from national and international granting agencies that will allow them to easily generate the starting materials and to analyze the results. A selection of their current grants is listed in their CVs (appendix), many of which will directly benefit from the pan-genome initiative. Chlamydomonas is usually the main if not sole research organism in the PIs' labs, so the proposal is clearly central to their research programs. The diversity of the subjects they study, from photosynthesis to cilia, from genome evolution to metal homeostasis, from transgenesis to synthetic biology, ensures that all aspects of Chlamydomonas biology will be covered in the analysis of the pan-genome. Several ongoing projects that will synergize with this pan-genome proposal can be highlighted. Population geneticist Rory Craig is generating assemblies of other algae, including 3 field isolates of C. reinhardtii that are not part of our sequencing request but that we would like JGI to annotate along with those they will assemble. This project targets TE dynamics in the species, the geographic structure of genetic diversity, gene flow, mutation rates and selection pressure (Craig et al., 2019). Co-PIs Marc Hanikenne, Pierre Cardol, Tom Druet and Denis Baurain, all from Liège University, are generating a MAGIC (Multiparent Advanced Generation Inter-Cross) population to fine- map quantitative traits. They crossed 8 starter strains (7 field isolates and 1 laboratory strain), all of which present interesting phenotypic characteristics and are part of our assembly/annotation request. The crossing scheme is designed so that all segments of each parental genome will be equally represented in the final population which they have finalized at 768 recombinant lines. Illumina sequencing was used to map the variants (Fig. 1), but the high genetic diversity of the field isolates (up to 2-3% at the
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SNP/short indels level) makes the mapping to a single reference genome inadequate to capture the entire spectrum of variants. They would therefore greatly benefit from assembled parental genomes and a high quality annotation.
Figure 1: the MAGIC design (left) and preliminary results of Illumina sequencing (right) illustrating chromosome-scale variations in the proportions of reads representing each of the parents (average contributions 10.3-15.6% each)
The goal of their MAGIC project is to correlate sequence variants with quantitative traits measured in the parents and in each member of the recombinant population. Among the traits are a host of photosynthetic parameters deduced from the analysis of chlorophyll a fluorescence induction curves. The other target is metal homeostasis, approached by measuring elemental profiles and growth properties in media with limiting or excess metals. This population is meant to be stored frozen and distributed to laboratories interested in scoring other phenotypes (motility, mating, phototaxis, sensitivity to drugs are all easily scored in plate format). Other ongoing programs that will benefit from the pan-genome include the analysis a family of ~40 fast-evolving repetitive proteins (Boulouis et al., 2015) that affect chloroplast transcript stability, possibly sequence-specific endoribonucleases (Vallon); the search for variants in epigenetic processes that may provide tools for transgene expression and reveal algal-specific pathways (Bock, Schroda); discovery of new regulatory elements that could be used for synthetic biology (Smith, Schroda); control of cilia biogenesis and swimming behavior by multi-gene networks (Dutcher); variants in photoprotective mechanisms which may be linked to photic niche adaptations (Niyogi); the importance of gene neighborhoods (Blaby-Haas); variability in mating type structure that may affect sexuality (Dutcher) ……
Technical Challenges: PacBio sequencing and genome assembly have proven very efficient in Chlamydomonas, and the wealth of transcriptome and homology data, combined with the expertise JGI has developed in this domain, should lead to excellent structural annotation (Blaby et al., 2014). The major technical difficulty that the proposal may have to face is the collection of new C. reinhardtii isolates from locations other than those
4 already sampled (NE-USA and Quebec, Japan). We plan to explore locations in France, England, Germany, Belgium, California and New Zealand. Collecting field isolates of green algae ("aceto-flagellates") is not difficult, and protocols are available that can be handled by undergraduate students, e.g. (Sack et al., 1994). Soil samples are left to germinate and individual clones are obtained from colonies by limiting dilution on agar plates. We cannot predict the frequency at which Chlamydomonas will be found among the algae, but throughput can be increased using PCR assays. We are currently validating a PCR assay based on plastid sequences. Final characterization as a bona fide C. reinhardtii will involve crossing to reference strains, which will be undertaken by the laboratory isolating the strain and can also be brought to medium throughput in 96- well format. An additional difficulty is to obtain axenic cultures, but luckily Chlamydomonas in addition to being phototrophic, is insensitive to potent antibacterial and antifungal agents that can be used to generate axenic cultures (Wang et al., 2016). We anticipate that some locations will not yield C. reinhardtii field isolates, but this will not be a problem as the diversity already available is large enough to justify a thorough exploration. It is not impossible that new species closely related to C. reinhardtii appears in this screen, which would be precious for our project or future ones.
Starting Materials: Strains will be cloned immediately prior to DNA isolation. Samples will be prepared in the laboratory of co-PI Susan Dutcher, who served as the head of the McDonnell Genome Institute at Washington University and has extensive experience in the preparation of high quality DNA from Chlamydomonas (Lin et al., 2013). Although several other partners would be able to carry out this process, we consider that grouping all manipulations in a single lab will ensure repeatable high quality. Our procedure will conform to the JGI Sample Preparation Requirements. The amounts needed are expected to be around 200 µg, which will be attainable with small scale cultures (<1L). DNA will be prepared from live cells after autolysin treatment to remove the cell wall, and use the NEB Monarch HMW DNA Extraction Kit. Quality control will use the Qubit for quantitation, Nanodrop for purity and Agilent Femto Pulse for size determination (Fig. 2). We pledge to only deliver pure and high MW DNA.
Figure 2: Femto Pulse trace of a typical Chlamydomonas DNA sample from the Dutcher lab.
For the strains already available, we expect shipment of the DNA, in tubes and according to JGI shipping specifications, within 2 months of approval of the project.
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C) Project Description i. Introduction The study of single gene traits was the foundation of modern genetics (Morgan, 1911). However, over the intervening century, it has become clear that many important traits are the result of extensive genetic variation and the interactions of both the variants with each other and with the environment. Understanding how different DNA sequences are translated into a range of complex phenotypes remains a key question in biology. Identifying the whole spectrum of genetic variation not only is important for the understanding of natural selection and evolution, it will also help us harnessing the products of billions of years of natural evolution to help man survive on an exhausted planet, while preserving some of its astounding biodiversity. Chlamydomonas reinhardtii (hereafter Chlamydomonas) is a precious partner for us in this task, because it provides a unique set of tools to investigate questions related to the major threats we are facing: global warming by anthropic production of greenhouse gasses, and erosion of natural habitats and biodiversity. Chlamydomonas is being studied by a large and productive community of investigators who are poised to tackle society-related challenges. Since the early 1950's, it has served as a prime model organism for the study of photosynthesis, cilia motility and a growing number of fields in biology (Harris, 2009). In this proposal, we seek to develop a pan-genome for Chlamydomonas, i.e. a set of cross-referenced high quality genome assemblies for about 20 strains, covering as much as possible of the natural variability of the species. It will include a few well- studied laboratory strains and a majority of field isolates of worldwide geographical provenance. Such a pan-genome is necessary to develop the key resource to study natural variation, i.e. sets of recombinant inbred strains. For all major model organisms, recombinant inbred lines have helped to map genotype-phenotype relationships for many traits, for example in mice via the Collaborative Cross (Threadgill and Churchill, 2012), in flies via the DGRP (Mackay et al., 2012), in Arabidopsis (Atwell et al., 2010; Kover et al., 2009) and others. As an illustration, the mice from the Collaborative Cross have been used in over 26,000 publications, whilst the DRGP and the Arabidopsis MAGIC collections are cited in >500 and >1700 publications respectively. The popularity of Chlamydomonas as a model organism stems from the early development of genetic tools allowing easy mutant isolation and characterization (Sager, 1955). Most strains are haploid, which allows immediate expression of recessive phenotypes, while clonal growth allows massive production of mutant strains Hundreds of phenotypic screens run in dozens of laboratories have yielded thousands of well-characterized mutants, the most interesting of which are stored in an NSF- funded Chlamydomonas Resource Center hosted by the University of Minnesota (www.chlamycollection.org). The development of a rich toolbox for manipulation of the nuclear, chloroplast and mitochondrial genomes has enabled the functional characterization of thousands of genes, and an indexed collection of insertional mutants nearly covers the known gene space (Li et al., 2016). Very early on, full mastery of the sexual cycle allowed the mapping of mutations (Ebersold and Levine, 1959), then physical markers (Silflow et al., 1995), paving the way for vigorous genomics developments. The initial efforts of P. Lefebvre and C. Silflow at UMN to create DNA
6 banks and maps (Kathir et al., 2003), combined with the EST sequencing efforts of the Kazusa Institute (Asamizu et al., 2000) and of A. Grossman at the Carnegie Institution (Zhang et al., 2004), led to the sequencing of the genome by the Joint Genome Institute in 2003 (Grossman et al., 2003; Merchant et al., 2007). The genome assembly and its annotation have been improved several times since then (Blaby et al., 2014), culminating in the recent establishment of a highly contiguous genome assembly (version 6), annotated to carry 17,585 genes. In addition to the automatic sequence analysis of the JGI, the Phytozome-hosted genome holds a rich text annotation crafted by hundreds of experts over several annotation and reannotation efforts (https://phytozome-next.jgi.doe.gov/info/Creinhardtii_v5_6). All laboratory strains come from a zygote isolated by G.M. Smith in a potato field in Amherst, MA in 1945. Interest in the genomic diversity of Chlamydomonas was initially spurred by the need to develop polymorphic markers for molecular mapping. Efforts were made to identify wild isolates that would be highly polymorphic with respect to laboratory strains, yet easy to interbreed. The most widely used are the clonal pair S1D2 and S1C5, isolated in Minnesota, with a SNP density > 2% relative to the reference genome, which has allowed easy mapping of mutations via their linkage to molecular markers (Vysotskaia et al., 2001). Thirty-six field isolates are available at the Chlamydomonas resource center or other banks, collected over the years by the laboratories of G. Bell, E. Harris, P. Lefebvre and J. Jarvik in the North-Eastern part of America and by T. Nakada in Southern Japan. Illumina sequencing by the labs of I.M Ehrenreich (Jang and Ehrenreich, 2012), K. Saleh-Ashtiani (Flowers et al., 2015), S. Dutcher (Lin et al., 2013), S. Merchant (Gallaher et al., 2015) and R. Ness (Craig et al., 2019) has revealed an unexpectedly high genomic diversity. The proportion of variable sites between two isolates can be as high as 3% genome-wide, including significant variability in the coding space. Millions of high confidence variants have been called within genes, which makes this dataset a rich source of functional diversity. Note that at this level of divergence, mapping Illumina reads to a single reference genome becomes problematic, so that variant calling remains incomplete. Indeed, the proportion of the genome that is “callable” when mapping diverse strains to the reference genome is ~65% (Ness et al., 2015). The study of Flowers et al (Flowers et al., 2015) has found 13,992 genes within contigs that they assembled from reads that would not map to the reference genome. Highlighting their high diversity, comparison with the most recent annotation shows that 2,370 of these new proteins have a best hit that is longer than 100 residues and carries more than 4 mismatches. It is fair to say that the yet uncharted gene space of Chlamydomonas reinhardtii contains tens of thousands of gene variants, accumulated over millions of generations of evolution in allopatric pre-speciation conditions. Karyotype variants have even been identified (https://www.biorxiv.org/content/10.1101/2021.04.23.441226v2). JGI is in the process of releasing PacBio-based genome assemblies of strains CC-4532 (the new reference for the species) and CC-503 (formerly used as a reference but demoted on account of its high genome instability). Important for our project, a telomere-to telomere assembly of CC-1690 (aka 21gr, the standard strain for laboratories working on cilia and nitrogen metabolism) has been produced from Nanopore reads (O'Donnell et al., 2020), but it has not been annotated yet. The Dutcher group also has assembled a PacBio HiFi genome for CC-125, the parent of CC-503,
7 with telomere to telomere continuity. In addition, a high-quality genome is available for CC-2931, a very divergent wild isolate from North Carolina that has been assembled using PacBio Sequel reads. Presently, the Keightley laboratory is assembling PacBio- HiFi based genomes for three other wild isolates, CC-2342, CC-2344 (both from Pennsylvania) and CC-1952 (S1C5). And recently, PacBio-based assemblies of three close relatives of C. reinhardtii (C. incerta, C. schloesseri and Edaphochlamy debaryana) have been generated and annotated (Craig et al., 2021), which together with the genomes of more distantly related multicellular relatives (Tetrabaena socialis, Yamagishiella unicocca, Gonium pectorale, Volvox carteri) provides a solid background phylogeny for the Reinhardtinia clade to which all these fascinating algae belong. The list of scientific questions that the project will help address is extensive, and the letters of support that accompany this proposal show that it goes far beyond the motivations of the PIs directly involved in the project. As a model organism, Chlamydomonas is truly expanding, with more and more laboratories attracted to it by the development of its genetic and genomic resources. The population genetics dimension that the proposed project will bring to the model will no doubt further increase its attractiveness. Within its two traditional fields, chloroplast and cilia biology, we expect the pan-genome to help the community fine tune understanding of the workings and biogenesis of these complex machineries. Each of these systems involves thousands of components and each makes up more than 10% of the proteome (Merchant et al., 2007). Many of these proteins interact in very specific manners. The genetic diversity observed within the species is bound to generate multiple sources of potential maladaptation or novel behaviors, not only in such recombinant lines as constituted in the MAGIC population, but also, because of admixing, in natural populations. The cilia in Chlamydomonas are both sensory and motile, meaning that they are not only needed for swimming and for response to changes in light intensity and direction, they are also involved in membrane-mediated and peptide-mediated signaling, sexual reproduction and ectosome production (Ostrowski et al., 2011). This proposal and the associated ongoing MAGIC project will reveal how genetic diversity, anchored or not on specific adaptations, promotes ciliary functions. In addition to chloroplast biogenesis mentioned above, photoprotection is another domain where we expect large phenotypic variations: it is highly multifactorial and directly responsive to variations in the environment (Erickson et al., 2015). Beyond these classical fields we note that colleagues interested in photoreceptors, in interactions with other microorganisms such as bacteria or fungi, in cell cycle, production of hydrocarbons, cytoskeletal components, biotechnology etc also expressed interest in mining the field isolates and the pan-genome data for genotype- phenotype correlations. ii. Project narrative A wealth of preliminary data is guiding us to craft the most efficient approach towards a Chlamydomonas pan-genome. Over the years, Illumina sequencing data has been collected for the 36 presently available field isolates, all from N.-E. America or Japan (Craig et al., 2021; Flowers et al., 2015; Jang and Ehrenreich, 2012; Lin et al., 2013; Ness et al., 2016), as well as for many laboratory strains (Gallaher et al., 2015). This last study revealed that laboratory strains are genetic mosaics mixing two ancestral haplotypes, one of them being present over 1/4 of the genome. Thus even if
8 unknowingly, Chlamydomonas laboratories have had to deal with the complex genetic structure of the species from the beginning. The most recent analysis, led by collaborator R. Craig (Craig et al., 2019), reveals that in addition to the Japanese population, two North American lineages, NA1 and NA2, can be defined (Fig 2).
Figure 2: A): Neighbor‐joining tree of all 4-fold degenerated genomic sites (supposedly not subject to selection), with the threes clades colored blue (NA1), red (NA2) or yellow (JPN). All nodes had >70% bootstrap support. B): The first and second axes of the Principal Component Analysis. MA Massachusetts, PA Pennsylvania (two locations, PA1 & PA2), NC North Carolina, FL Florida, MN Minnesota, QC Quebec, Kg Kagoshima Prefecture. .
These lineages correlate well with geography, and specifically glacial refugia, supporting allopatric divergence within N. America. Broadly speaking, any two isolates from the same lineage differ at ~2% of sites genome-wide, while two isolates from different lineages differ at ~3%. Some evidence was found for migration from USA to Quebec (CC-3079), and signatures of admixture between NA1 and NA2 genomes were also observed, following a gradient along dimension PC1. Admixed haplotypes span up to 25 Mb in the lines studied. This implies that certain barriers to gene flow may exist (e.g. reproductive incompatibilities), since substantial genetic differences are maintained in the face of significant genetic exchange. The fact that the Japanese isolates, sampled thousands of miles away, remain interfertile with the North-American ones indicates that the species is ubiquitous and should be found in all sorts of temperate locations around the world. Altogether, these results suggest that a broader geographic sampling as proposed in this project will reveal an even higher diversity, while providing means to correlate genotype and phenotype at a finer scale. The main objective of this proposal is to correlate genotypes and phenotypes within the species. Variability in growth properties of laboratory strains has been studied by (Gallaher et al., 2015), and even greater variation is expected across field isolates. For example, the parents of the MAGIC population show high variability in their ability to perform Non Photochemical Quenching (NPQ), an essential photoprotection mechanisms for the photosynthetic apparatus, and the spread appears even higher in the recombinant lines (Fig 3).
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Figure 3: Non Photochemical Quenching measured in the parents (left) and recombinant lines (right), with across replicates variability of the population represented in the center.
Already, efforts have been made to estimate the effect of individual variants on gene function, based on the annotation of the reference (Flowers et al., 2015; Gallaher et al., 2015). With the advent of two more contiguous and better annotated genomes of laboratory strains (CC-503 v6 and CC-4532 v6), this effort can be carried further, but it is only with a full annotation of the field isolates that all differences can be captured and categorized. Our experimental plan will be split into two phases, one will deal with already established lines, and one will rely on the isolation of novel field isolates from additional worldwide locations. The first step will be to gather in the laboratory of S. Dutcher all the strains of Phase I, and clone them to prepare DNA from single colonies. Table I lists the strains, their origin and what is known about their genetic structure.
strain mating geographical MAGIC category assembly annotation note name type origin parent
CC-503 Lab + Massachusetts available v6 done Historical reference, JGI v5; demoted based on genome instability CC-4532 Lab - Massachusetts available v6 done New reference strain, JGI v6 CC-1690 Lab + Massachusetts available requested aka 21gr; Nanopore assembly by S. O'Donnell, polished with Illumina data CC-125 Lab + Massachusetts available requested The progenitor of CC-503; PacBio-based assembly by S. Dutcher CC-1009 Lab - Massachusetts requested requested With CC-1010, covers all haplotype 2 blocks CC-1010 Lab + Massachusetts requested requested y With CC-1009, covers all haplotype 2 blocks; unable to make Chl in the dark CC-2931 Field - North Carolina available requested y PacBio Sequel assembled by Rory Craig CC-410 Field - Caroline Islands requested requested y Chloroplast genome highly similar to that of lab strains CC-1418 Field - Florida requested requested y Gulliver transposon pattern similar to that of lab strains CC-2936 Field + Quebec requested requested y From Graham Bell, 1993; high NPQ in myxotrophy CC-2937 Field + Quebec requested requested y From Graham Bell, 1993; low NPQ in myxotrophy CC-1952 Field - Minnesota soon available requested y S1 C5, almost identical to S1 D2; used for molecular mapping CC-2344 Field + Pennsylvania soon available requested y From Jonathan Jarvik, 1989 CC-2342 Field - Pennsylvania soon available requested From Jonathan Jarvik, 1989 CC-3079 Field - Quebec requested requested From Graham Bell, 1994; Most similar to US, not Quebec, strains CC-1373 Field + Massachusetts requested requested aka "C. smithii"; the field isolate closest to the lab strains CC-2343 Field + Florida requested requested Has active Pioneer 1 transposition NIES-2463 Field + Japan requested requested Together with almost identical NIES-2464, forms the Japanese lineage
Chlamydomonas Cuba or SAG 7.73 - available done Assembled and annotated by R. Craig; in Phycocosm incerta Netherlands CCAP Chlamydomonas - Kenya available done Assembled and annotated by R. Craig; in Phycocosm 11/173 schloesseri CCAP Edaphochlamys - Czech Republic available done Assembled and annotated by R. Craig; in Phycocosm 11/70 debaryana
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Table I: list of genomes already available for the pan-genome, and of strains to be used in the Phase I assembly/annotation effort. The associated metadata for field isolates has been gathered by (Craig et al., 2019).
Phase II will be led in parallel by several of the laboratories involved and perhaps other laboratories from around the world that may volunteer once the project has started. We will start by collecting soil samples from cultivated fields (the favorite habitat of the species) that will be frozen or dried to select for the resistant zygospores of Chlamydomonas. Germination in the light will release the swimming phototrophs that can be further selected by phototaxis. Plating on mineral agar medium after serial dilution will reveal those able to form colonies. Alternatively, colonies can be retrieved by germination of zygotes, which would ensure that both mating types are collected. Experiments are underway to design a simple clade-specific colony PCR assay that will tease apart potential C. reinhardtii from the other species of the genus and from the remaining green flagellates. The assay will be performed in plate format and scored by gel electrophoresis. Finally, the verification by mating that the strain is interfertile with mt+ or mt- tester strains and yields viable progeny will provide proof that we have isolated a true C. reinhardtii strain. Illumina sequencing will be used to determine how different they are from the strains already available, and to choose which ones should be chosen for downstream analysis. Axenization will be obtained by antibiotic treatment, but we will pay attention to obligate association with bacteria as they may sign metabolic interactions. Once a sufficient number of strains have been collected to complete our design, they will be shipped to the laboratory of S. Dutcher for DNA preparation and Phase II sequencing by JGI. In parallel, they will be transferred to the Chlamydomonas Resource Center at the University of Minnesota, along with associated metadata (location and time of sampling, morphological and phenotypic observations, mating type) for storage and later for distribution. While it is difficult to commit on the precise date at which Phase II strains will be ready, we know that the protocols used are reliable. The large size of our group, the support we enjoy in the community and the enthusiasm with which the project is received should speed up realization of this task. We conservatively give ourselves a limit of two years after start of the project, at which time we would decide on the set of strains to be submitted to JGI as Phase II. Our plan is to submit 10 strains, but we may reduce this number if the genetic diversity is below our expectations. Diversity will be assessed by low coverage (5x) multiplex Illumina sequencing. An additional aspect of the project is the generation of transcriptome data. A large fraction of phenotypic variations is expected to be borne by differences not so much in the sequence of the proteins rather in the expression patterns of the genes. The underlying mechanisms (promoter strength, binding of transcription factors, splicing efficiency, methylation status, alternative splicing, etc) will be revealed only by cross-analysis of multiple data sets, including transcriptomics. A complete description of gene expression patterns in all the strains at hand is outside the scope of the project. Nevertheless, we plan to isolate RNA under diverse conditions from all of our strains for later transcriptome analysis. We only request Illumina or IsoSeq sequencing for 3 Phase I and 6 Phase II strains, in each case of 3 RNA samples : one in phototrophy (growth in high light on mineral medium), one in heterotrophy (growth in
11 the dark on acetate-supplemented medium) and one following deciliation by an acid shock. The RNA samples will be generated in the laboratories of S. Merchant and S. Dutcher. Collecting transcriptome data is important for structural annotation because we know already from prior work that even for laboratory strains the divergence between haplotypes is sufficiently high to affect the mapping of reads. Therefore, existing transcriptomic datasets, while extensive, will be inadequate for complete structural annotation.
We will rely on JGI to perform PacBio sequencing and genome assembly. If needed, further scaffolding of the contigs into chromosomes will be facilitated by the availability of a telomere-to-telomere assembly of CC-1690 (O'Donnell et al., 2020), a laboratory strain widely used by the community. We also request some HiC analysis for all assemblies of field isolates. By incorporating the physical distance between sites on the genome, it is a powerful approach to improve scaffolding and test the synteny of our genomes. While interfertility of the strains would suggest high synteny between the genomes, we cannot rule out that HiC reveals large rearrangements in some of the field isolates. For example the CC-2931 assembly harbors three putative reciprocal translocations. Such situations can potentially confound genetic analysis, which calls for careful scaffolding and independent tests of the assembly at long range. We will also ask JGI to analyze their PacBio data for DNA methylation, both on C and A bases. DNA methylation, although relatively infrequent, in C. reinhardtii, is a reliable marker for the chromatin status and 5mC and 6mA profiles help define transcriptionally silent regions and promoters, respectively. If needed, the consortium may generate Nanopore data that can also be used to directly call the methylation status of genomic sites. ChIP analysis, although extremely powerful for epigenetic analysis, is beyond the scope of this proposal. An important aspect of the work will be the assembly and annotation of the organelle genomes. Due to their polyploidy, especially for the chloroplast, organelle- derived reads are often treated separately from the nuclear ones. We ask JGI to pay specific attention to these genomes, because Chlamydomonas research both historically and today places strong emphasis on the interplay between the organelle and nuclear genomes. Together they shape such central functions as photosynthesis, cofactor and lipid biosynthesis, and oxidative phosphorylation. Once the data has been obtained, we will make it immediately available to the entire community for analysis. Each genome and its annotation will be displayed in Phycocosm (https://phycocosm.jgi.doe.gov/), allowing full search, blast and download. The power of this proposal however lies in the detailed comparison that it allows among strains. For example, we want to be able to automatically retrieve all sequences associated with a locus and compare them among strains. To facilitate such operations, we ask that JGI apply their lift over pipeline, as they have done between versions of the genome and between CC-503 and CC-4532, to identify orthologous loci across strains. Each locus in each strain will be identified by a locus ID, in the form ssss_cc_nnnnn, where ssss is the strain number at the Chlamydomonas Resource Center, cc is the chromosome (contig) number and nnnnn is the number of the orthologous locus in the reference annotation (CC-4532). The
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number is odd for genes on the top strand, even for genes on the bottom strand. For strain-specific genes, a new nnnnn number will be created based on the neighboring genes. A synteny browser is necessary to allow visual inspection of the genes and analyze structural variants, alternative splicing, methylation status, expression pattern etc. We are currently using the UCSC Gbrowse structure. The database and browser should be flexible, allowing easy integration of new genomes and user-generated data in the form of browser tracks or annotations. Among related projects, the comparative database structures for Paramecium (https://paramecium.i2bc.paris-saclay.fr), yeast (http://1002genomes.u-strasbg.fr/ ) or Diatoms (https://www.diatomicsbase.bio.ens.psl.eu/) are being explored as models. At a later stage, and if the data usage by the community shows that such an effort will have lasting value, we will seek support to represent the pan-genome graphically, using the complex and powerful tools that are being generated by the graph genomics community, e.g. the vg toolkit, (Garrison et al., 2018).
iii. Roles and responsibilities of the project team
Our project groups 18 participants (15 PIs and 3 key collaborators) who all took part in the creation of the proposal and will play an active role in its realization: Role Name main domains of competence country PI Olivier Vallon Photosynthesis; chloroplast; genomics France Co-PI Krishna Niyogi Photosynthesis; redox USA Co-PI Sabeeha Merchant Photosynthesis; metal homeostasis; genomics USA Co-PI Susan K. Dutcher Cilia; genomics USA Co-PI Crysten Blaby-Haas Functional genomics USA Co-PI Marc Hanikenne Metal homeostasis Belgium Co-PI Baurain Denis Genomics Belgium Co-PI Pierre Cardol Photosynthesis Belgium Co-PI Tom Druet Genomics Belgium Co-PI Alison Smith Vitamins; synthetic biology UK Co-PI Michael Schroda Protein homeostasis; synthetic biology Germany Co-PI Ralph Bock Chloroplast; synthetic biology Germany Co-PI Robert Ness Population genomics Canada Co-PI Pete Lefebvre Genomics; field isolates; cilia USA Co-PI Carolyn Silflow Genomics; field isolates; basal body USA Collaborator Rory Craig Population genomics; transposable elements UK Collaborator Samuel O'Donnell Genomics New Zealand Collaborator Sean Gallaher Genomics USA
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All the PIs involved in this project share a deep interest in its completion and dissemination. They can be considered as representative of entire spectrum of the Chlamydomonas research community, either by subject or by nation. The consortium will meet by video-conference every three months, PI O. Vallon presiding, to monitor progress and deal with technical and other challenges. We will invite the JGI program manager and any other JGI staff whose expertise will be needed. Every other year, most members of the team will meet in person at the Chlamydomonas conference, where a specific pan-genome workshop will be held. Decisions such as quality control, launching Phase II, vetting annotations etc will be based on consensus, after thorough examination of the state of the data. iv. Anticipated schedule of project milestones
Mo 3: Phase I DNA samples shipped Mo 9: first assemblies generated Mo 12: scaffolding complete to chromosome level Mo 16: structural annotation of genes and TEs complete Mo 18: Phase I genomes available on Phycocosm; start of building comparative genome database Mo 24: collection of new field isolates complete. Milestone paper Mo 26: Phase II DNA samples shipped Mo 34: Phase II assemblies completed and scaffolded Mo 38: Phase II annotations complete, genomes deposited in Phycocosm Mo 42: Pan-genome database fully functional and publicly available. First analysis papers come out. v. The size and nature of the larger community that will use the data
In this composite image of Chlamydomonas, used by PIs S. Dutcher and O. Vallon for the introduction to a special issue of Genetics that was devoted to the analysis of the Chlamydomonas genome (Vallon and Dutcher, 2008), each pixel is a picture of a Chlamydomonas researcher or a figure from a Chlamydomonas paper. There are currently ~ 100 labs in the world that use Chlamydomonas as their main or sole research organism, and every year between 400 and 450 papers are published that deal with this organism. Every other year since the early 1980's, the International Conference on the Cell and Molecular Biology of Chlamydomonas gathers hundreds of participants from around the world, and the upcoming meeting (Chlamy 2020+1, https://chlamy2020.sciencesconf.org/), organized by PI O. Vallon, promises to draw a large crowd and
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provide an exceptional scientific program. Genomics has now entered all our ways of thinking, and it holds a prominent place at our meetings. Based on the overwhelmingly favorable response of our colleagues when we started collecting letters of support, we can state that the community is ready to use the pan-genome data: they all plan to mine for variants in the genes/pathways of interest, and many also consider using the MAGIC collection for high throughput screens and QTL discovery. The areas in which they plan to apply the pan-genome include metabolism (Salehi-Ashtiani), CO2 concentration (Mackinder; McCormick), chloroplast gene expression and medical biotechnology (Nickelsen), adaptation and biotechnology (Rochaix, Grosman, Molnar), production of hydrocarbons (Lea-Smith), photoreceptors (Hegemann), light-sensing and bacterial interactions (Mittag), cytokinesis (Onishi), cytoskeletal functions (Avasthi), cell cycle (Umen), peptidergic signaling (King), evolution of repeated sequences (Day) etc…
vi. Relevance to DOE missions
The importance of Chlamydomonas research for the missions of the DOE is long established. As a testimony, the Chlamydomonas genome is one of the 8 flagship genomes (and the only alga) in Phytozome. Since the early 2000's, the JGI-led Chlamydomonas genome project has served as a unifying line in the community. This was one of the goals of the expert annotation project that led to the 2007 Science paper (Merchant et al., 2007). It was co-authored by dozens of members of the community, including almost all the PIs in this proposal, along with many prominent JGI members, including D. Rokhsar, I. Grigoriev, D. Goodstein, S. Prochnik, J. Schmutz, A. Salamov, J.Grimwood, and others. This collaboration with JGI has been a tremendous boost to Chlamydomonas research, enabling the steady growth of the community and a widening of the subject areas in which Chlamydomonas is used.
How does Chlamydomonas research help DOE address current and future energy and environmental challenges? The answer lie largely in its ability to use sunlight to create biological matter. Photosynthesis, the light-driven conversion of CO2 into carbohydrates, is a major field of research for the Chlamydomonas community. This alga is the only photosynthetic eukaryote in which all three genomes (nuclear, chloroplast, mitochondrial) can be genetically transformed (Rochaix, 1995). Thanks to its microbial lifestyle and metabolic plasticity, Chlamydomonas allows easy generation and characterization of mutants. Among these, mutants unable to perform photosynthesis have been of tremendous help to dissect the workings of this highly elaborate pathway and its regulation. Chlamydomonas is as essential to the study of bioenergetics, as mouse is to medical research. With atmospheric CO2 concentration and global temperature rising at a dramatic pace, mitigating, or even limiting, the accumulation of greenhouse gasses is a survival question for humanity. To reach this goal, a deeper understanding of photosynthesis and CO2 fixation is required, and Chlamydomonas has an essential role to play.
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D) References:
Asamizu, E., Miura, K., Kucho, K., Inoue, Y., Fukuzawa, H., Ohyama, K., Nakamura, Y., and Tabata, S. (2000). Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii. DNA research : an international journal for rapid publication of reports on genes and genomes 7, 305-307. Atwell, S., Huang, Y.S., Vilhjalmsson, B.J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A.M., Hu, T.T., et al. (2010). Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465, 627-631. Blaby, I.K., Blaby-Haas, C.E., Tourasse, N., Hom, E.F., Lopez, D., Aksoy, M., Grossman, A., Umen, J., Dutcher, S., Porter, M., et al. (2014). The Chlamydomonas genome project: a decade on. Trends in plant science 19, 672-680. Boulouis, A., Drapier, D., Razafimanantsoa, H., Wostrikoff, K., Tourasse, N.J., Pascal, K., Girard- Bascou, J., Vallon, O., Wollman, F.A., and Choquet, Y. (2015). Spontaneous dominant mutations in Chlamydomonas highlight ongoing evolution by gene diversification. The Plant cell 27, 984- 1001. Craig, R.J., Bondel, K.B., Arakawa, K., Nakada, T., Ito, T., Bell, G., Colegrave, N., Keightley, P.D., and Ness, R.W. (2019). Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii. Molecular ecology 28, 3977-3993. Craig, R.J., Hasan, A.R., Ness, R.W., and Keightley, P.D. (2021). Comparative genomics of Chlamydomonas. The Plant cell, doi: 10.1093/plcell/koab1026. Ebersold, W.T., and Levine, R.P. (1959). A genetic analysis of linkage group I of Chlamydomonas reinhardi. Zeitschrift fur Vererbungslehre 90, 74-82. Erickson, E., Wakao, S., and Niyogi, K.K. (2015). Light stress and photoprotection in Chlamydomonas reinhardtii. The Plant journal : for cell and molecular biology 82, 449-465. Flowers, J.M., Hazzouri, K.M., Pham, G.M., Rosas, U., Bahmani, T., Khraiwesh, B., Nelson, D.R., Jijakli, K., Abdrabu, R., Harris, E.H., et al. (2015). Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii. The Plant cell 27, 2353-2369. Gallaher, S.D., Fitz-Gibbon, S.T., Glaesener, A.G., Pellegrini, M., and Merchant, S.S. (2015). Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies. The Plant cell 27, 2335-2352. Garrison, E., Siren, J., Novak, A.M., Hickey, G., Eizenga, J.M., Dawson, E.T., Jones, W., Garg, S., Markello, C., Lin, M.F., et al. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature biotechnology 36, 875-879. Grossman, A.R., Harris, E.E., Hauser, C., Lefebvre, P.A., Martinez, D., Rokhsar, D., Shrager, J., Silflow, C.D., Stern, D., Vallon, O., et al. (2003). Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryotic cell 2, 1137-1150. Harris, E.H. (2009). The Chlamydomonas sourcebook. (San Diego, CA: Academic Press). Jang, H., and Ehrenreich, I.M. (2012). Genome-wide characterization of genetic variation in the unicellular, green alga Chlamydomonas reinhardtii. PloS one 7, e41307. Kathir, P., LaVoie, M., Brazelton, W.J., Haas, N.A., Lefebvre, P.A., and Silflow, C.D. (2003). Molecular map of the Chlamydomonas reinhardtii nuclear genome. Eukaryotic cell 2, 362-379.
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Kover, P.X., Valdar, W., Trakalo, J., Scarcelli, N., Ehrenreich, I.M., Purugganan, M.D., Durrant, C., and Mott, R. (2009). A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS genetics 5, e1000551. Li, X., Zhang, R., Patena, W., Gang, S.S., Blum, S.R., Ivanova, N., Yue, R., Robertson, J.M., Lefebvre, P.A., Fitz-Gibbon, S.T., et al. (2016). An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. The Plant cell 28, 367-387. Lin, H., Miller, M.L., Granas, D.M., and Dutcher, S.K. (2013). Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii. PLoS genetics 9, e1003841. Mackay, T.F., Richards, S., Stone, E.A., Barbadilla, A., Ayroles, J.F., Zhu, D., Casillas, S., Han, Y., Magwire, M.M., Cridland, J.M., et al. (2012). The Drosophila melanogaster Genetic Reference Panel. Nature 482, 173-178. Merchant, S.S., Prochnik, S.E., Vallon, O., Harris, E.H., Karpowicz, S.J., Witman, G.B., Terry, A., Salamov, A., Fritz-Laylin, L.K., Marechal-Drouard, L., et al. (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245-250. Morgan, T.H. (1911). Random Segregation Versus Coupling in Mendelian Inheritance. Science 34, 384. Ness, R.W., Kraemer, S.A., Colegrave, N., and Keightley, P.D. (2016). Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in the Chlamydomonas reinhardtii Plastid Genome. Mol Biol Evol 33, 800-808. Ness, R.W., Morgan, A.D., Vasanthakrishnan, R.B., Colegrave, N., and Keightley, P.D. (2015). Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii. Genome research 25, 1739-1749. O'Donnell, S., Chaux, F., and Fischer, G. (2020). Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690. Microbiology resource announcements 9. Ostrowski, L.E., Dutcher, S.K., and Lo, C.W. (2011). Cilia and models for studying structure and function. Proceedings of the American Thoracic Society 8, 423-429. Rochaix, J.D. (1995). Chlamydomonas reinhardtii as the photosynthetic yeast. Annu.Rev.Genet. 29, 209-230. Sack, L., Zeyl, C., Bell, G., Sharbel, T., Reboud, X., Bernhardt, T., and Koelewyn, H. (1994). Isolation of four new strains of Chlamydomonas reinhardtii (Chlorophyta) from soil samples. J. Phycol. 30, 770-773. Sager, R. (1955). Inheritance in the Green Alga Chlamydomonas Reinhardi. Genetics 40, 476- 489. Silflow, C.D., Kathir, P., and Lefebvre, P.A. (1995). Molecular mapping of genes for flagellar proteins in Chlamydomonas. Methods Cell Biol. 47, 525-530. Threadgill, D.W., and Churchill, G.A. (2012). Ten years of the collaborative cross. G3 2, 153-156. Vallon, O., and Dutcher, S. (2008). Treasure hunting in the Chlamydomonas genome. Genetics 179, 3-6. Vysotskaia, V.S., Curtis, D.E., Voinov, A.V., Kathir, P., Silflow, C.D., and Lefebvre, P.A. (2001). Development and characterization of genome-wide single nucleotide polymorphism markers in the green alga Chlamydomonas reinhardtii. Plant physiology 127, 386-389.
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Wang, L., Yang, F., Chen, H., Fan, Z., Zhou, Y., Lu, J., and Zheng, Y. (2016). Antimicrobial cocktails to control bacterial and fungal contamination in Chlamydomonas reinhardtii cultures. BioTechniques 60, 145-149. Zhang, Z., Shrager, J., Jain, M., Chang, C.W., Vallon, O., and Grossman, A.R. (2004). Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryotic cell 3, 1331-1348.
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Personal details Gender Male Name and first name: VALLON Olivier Country France Current position Function Directeur de Recherche 2ème classe - CNRS Appointment(s) in research/teaching organisation(s) Organisation Department Laboratory Postcode Town CNRS IBPC UMR7141 75005 Paris Other public or private organisation(s) Organisation Position Town Country
Previous positions Start date End date Town Organisation Function 1981 1982 Amiens, FR Education Nationale Science teacher 1986 1987 Copenhagen, DK Carlsberg Laboratory post-doc 1987 1989 Cambridge, MA Harvard University post-doc 1989 1990 Paris, FR CNRS, Institut Jacques Monod, CR2 1990 1992 Paris, FR CNRS, Institut de Biologie Physico-Chimique CR2 1992 2002 Paris, FR CNRS, Institut de Biologie Physico-Chimique CR1 2002 2003 Stanford, CA Carnegie Institution of Washington Sabbatical 2002 - Paris, FR CNRS, Institut de Biologie Physico-Chimique DR2 2016 2019 Paris, FR CNRS, GdR3422 Directeur Career interruption(s)
Education CAPES de Sciences Naturelles, 1981 Agrégation de Sciences Naturelles, 1982 Doctorat de l'Université Pierre et Marie Curie, 1986 Habilitation à Diriger des Recherches, 1996 Scientific products Grants, prizes, awards, fellowships, etc. ANR Blanc GenomeChlamy (2005-2008), coordinator ANR Blanc Algomics (2009-2012), co-PI European FP7 grant GIAVAP (2011-2014), co-PI ANR Blanc ChloroRNP (2013-2016) (major participant) Two Procope French-German collaboration grants, one FIST French-American. 71 publications in international peer-reviewed journals. ISI-core H-index: 30, average citation/year: 142 5 publications most relevant to the proposal What is the major contribution of this publication? 1 Cavaiuolo, M., Kuras, R., Wollman, F. A., Choquet, Y., and Vallon, This is the first nt-level transcriptome map of the Chlamydomonas O. (2017) Small RNA profiling in Chlamydomonas: insights into chloroplast. Use of sRNA and stranded sequencing allowed us to chloroplast RNA metabolism. Nucleic acids research 45, 10783- study cp RNA processing and degradation in great detail 10799 2* Blaby, I. K., Blaby-Haas, C. E., Tourasse, N., Hom, E. F., Lopez, D., This paper described version 4 of the genome, detailing the efforts Aksoy, M., Grossman, A., Umen, J., Dutcher, S., Porter, M., King, done to fill in the gaps, improve the annotation etc… It shows how S., Witman, G. B., Stanke, M., Harris, E. H., Goodstein, D., much the community was involved in the process of improving the Grimwood, J., Schmutz, J., Vallon, O., Merchant, S. S., and genomic resources in Chlamydomonas. Prochnik, S. (2014) The Chlamydomonas genome project: a decade on. Trends in plant science 19, 672-680 3* Palenik, B., Grimwood, J., Aerts, A., Rouze, P., Salamov, A., For this paper, I participated in the annotation of the Ostreococcus Putnam, N., …, Merchant, S. S., …., Vallon, O., … Paulsen, I., lucimarinus genome to which co-PI S. Merchant also contributed. My Delwiche, C., Schmutz, J., Rokhsar, D., Van de Peer, Y., Moreau, input was minor, but it ushered me into algal genomics at large, H., and Grigoriev, I. V. (2007) The tiny eukaryote Ostreococcus which led me eventually to lead the assembly and annotation effort provides genomic insights into the paradox of plankton on Lobosphaera incisa (manuscript in preparation) speciation. Proceedings of the National Academy of Sciences of the United States of America 104, 7705-7710 4* Merchant, S. S., Prochnik, S. E., Vallon, ….., Grimwood, J., This is the founding paper of Chlamydomonas genomics. With S. Schmutz, J., Cardol, P., ……, Dutcher, S.,….., Hanikenne, M., ….. Merchant, I led the team of annotaters of the genome, which gave Niyogi, K., ….., Schroda, M., …., Grigoriev, I. V., Rokhsar, D. S., and me a prominent role in Chlamydomonas genomics. Several genome Grossman, A. R. (2007) The Chlamydomonas genome reveals the versions and update papers have followed, the last one on v6 being evolution of key animal and plant functions. Science 318, 245- written with Rory Craig as lead author. With him, I am also writing the 250 Genome chapter in the Chlamydomonas Source book, 3rd ed. 5* Grossman, A. R., Harris, E. E., Hauser, C., Lefebvre, P. A., The first paper summarizing Chlamydomonas genomic efforts, mostly Martinez, D., Rokhsar, D., Shrager, J., Silflow, C. D., Stern, D., centered on DNA libraries, EST collections, microarrays etc.. It Vallon, O., and Zhang, Z. (2003) Chlamydomonas reinhardtii at coincided with my sabbatical stay in Arthur Grossman's lab at the the crossroads of genomics. Eukaryotic cell 2, 1137-1150 Carnegie and my first involvement with Chlamydomonas genomics 5 other publications of interest What is the major contribution of this publication? 6 Salinas-Giege, T., Cavaiuolo, M., Cognat, V., Ubrig, E., Remacle, This paper demonstrated polycytidylation of mt mRNAs in C., Duchene, A. M., Vallon, O., and Marechal-Drouard, L. (2017) Chlamydomonas. It was a collaboration with the Drouard lab in Polycytidylation of mitochondrial mRNAs in Chlamydomonas Strasbourg and started a collaboration on mt OPRs that continues reinhardtii. Nucleic acids research 45, 12963-12973 today. 7 Wei, L., Derrien, B., Gautier, A., Houille-Vernes, L., Boulouis, A., This paper is a comprehensive description of how the photosynthetic Saint-Marcoux, D., Malnoe, A., Rappaport, F., de Vitry, C., Vallon, apparatus of Chlamydomonas responds to nitrogen starvation. We O., Choquet, Y., and Wollman, F. A. (2014) Nitric Oxide-Triggered showed that degradation of cytochrome b6f was govered by NO Remodeling of Chloroplast Bioenergetics and Thylakoid Proteins (which also controls induction of the L-amino acid oxidase). upon Nitrogen Starvation in Chlamydomonas reinhardtii. The Plant cell 26, 353-372 8 Boulouis, A., Drapier, D., Razafimanantsoa, H., Wostrikoff, K., This paper describes mutations in two OPR proteins that lead to Tourasse, N. J., Pascal, K., Girard-Bascou, J., Vallon, O., Wollman, specific destabilization of two chloroplast mRNAs. We proposed that F. A., and Choquet, Y. (2015) Spontaneous dominant mutations the RAP domain found at their C-terminus acts as an in Chlamydomonas highlight ongoing evolution by gene endoribonuclease. The NCL family they belong to evolves under diversification. The Plant cell 27, 984-1001 positive selection. Their diversity in field isolates is high, suggesting a role in speciation through nucleo-chloroplastic incompatibilities. 9 Takahashi, H., Clowez, S., Wollman, F. A., Vallon, O., and In this paper, in an exciting collaboration with the late F. Rappaport, Rappaport, F. (2013) Cyclic electron flow is redox-controlled but we showed by using mutants and combined biophysics/biochemical independent of state transition. Nature communications 4, 1954- measurements the disjunction of state transitions and cyclic electron 1961. flow in Chlamydomonas, 10 Majeran, W., Wollman, F. A., and Vallon, O. (2000) Evidence for a Using translational attenuation, we knocked down expression of an role of ClpP in the degradation of the chloroplast cytochrome essential chloroplast gene clpP1, and showed that it led to a b(6)f complex. The Plant cell 12, 137-150 stabilization of cytochrome b6f during nitrogen starvation Other activities Executive board, supervision of students, teaching, memberships in panels or individual scientific reviewing activities… Within UMR7141, I lead the research theme: Genetics and Genomics of Microalgae Director of the Groupement de Recherche "Organismes Photosynthétiques", GdR3422 (2016-2020) Board member, Groupement de Recherche "Integrative Biology of CO2 fixation", GdR2104 (2021-2025) Board member, LABEX Dynamo Organizer of 19th International Conference on the Cell and Molecular Biology of Chlamydomonas (Chlamy 2020+1) Member of the Comité National LUMIERE & SOCIETE Editorial board member of Plants (MDPI). Reviewer of approx 10 papers/year, for PNAS, EMBO J., Science Advances, Frontiers, Euk. Cell, Plant Cell, Plant Physiol., Plant Cell Physiol., Plant J., Plants, JexBot., Nucleic Acids Res., RNA Biol., Biochim Biophys. Acta, Plos Genetics, G3, J. Bac, Res. Microbiology, mSphere, BMC Genomics, J. Phycol, Protist, Marine Drugs, Anal. Biochem etc.Grant reviewer for INRA, ANR, KAUST University, University of Minnesota, Région Rhone-Alpes Research interests Please briefly describe your research activities over the last 10 years I am deeply involved with Chlamydomonas genomics. I organize regular updates of the expert annotation, involving a large number of experts working in the very diverse fields where Chlamydomonas is being used as a model. I am currently working on the release of version 6, to which the community is also associated. In collaboration, I have studied the subtelomeric regions and their unusual repeats, in C. reinhardtii and other green algae; alternative splicing; the snoRNAs; intracellular protein targeting. I have also characterized the transcriptomes of the Chlamydomonas organelles, chloroplast and mitochondrion, and revealed hitherto overlooked specificites of their RNA metabolism. I am the main organizer of the Chlamydomonas meeting Chlamy 2020+1 which this year will take place in France. I have assembled and annotated the genome the Trebouxiophyceae Lobosphaera incisa, in the framwork of the European project GIAVAP. I also work on the genome of the colorless alga Polytomella (5 species), a close relative of C. reinhardtii that has lost photosynthesis and the chloroplast genome. I use photosynthesis mutants to study the biogenesis of the photosyntetic apparatus in Chlamydomonas. This has led me to systematically study two families of repeat proteins, the PPRs and OPRs. Among the latter, I have identified a subfamily of putative sequence-specific endoribonucleases. I have also studied the regulation and mechanisms of the remodeling of the photosynthetic apparatus under nitrogen starvation. In particular, my work on the chloroplast protease ClpP has unravaled some of its targets, specificities of its biogenesis and recently its structure via cry-EM. In the field of photosynthesis, I have studied the relationship between state transitions and cyclic electron flow, with emphasis on the role of the PETO protein
BIOGRAPHICAL SKETCH – SABEEHA MERCHANT (3/2021)
Education and Training University of Wisconsin Molecular Biology B.S. 1979 University of Wisconsin Biochemistry Ph.D. 1983 Harvard University Cell&Dev Biology post-doc 1984-87
Research and Professional Experience Present 2019-present Warren C. Eveland Endowed Chair in Biological Sciences, University of California, Berkeley Faculty Senior Scientist, Lawrence Berkeley National Laboratory, Berkeley, CA 2018-present Distinguished Professor, Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California – Berkeley Adjunct Distinguished Professor, Department of Chemistry and Biochemistry, UCLA 2015–present External member, Max Planck Institut-Molecular Plant Physiology, Potsdam-Golm Previous 1987–2018 Assistant to Distinguished Professor, Department of Chemistry & Biochemistry, University of California, Los Angeles 1998 Visiting Professor, University of Basel, Basel, Switzerland. 2000-2009 Chair, Molecular Biology Inter-Departmental Ph.D. Program 2001–2009 Associate Director including Acting Director 2004-2005, Molecular Biology Institute, University of California, Los Angeles 2007-2014 Associate Director, Cell and Molecular Biology training program 2014–2018 Director, UCLA-DOE Institute for Genomics and Proteomics, David Geffen School of Medicine, University of California, Los Angeles
Publications (10 most closely related to the proposed project) Terauchi, A.M., Lu, S.F., Zaffagno, M., Tappa, S., Hirasawa, M., Tripathy, J.N., Knaff, D.B., Farmer, P.J., Lemaire, S., Hase, T., Merchant, S.S. (2009) Pattern of Expression and Substrate Specificity of Chlamydomonas Chloroplast Ferredoxins. J. Biol. Chem. 284:25867-25878. http://www.jbc.org/content/284/38/25867.full.pdf Page, M.D., Allen, M.D., Kropat, J., Urzica, E., Karpowicz, S., Hsieh, S.I., Loo, J.A., Merchant, S.S. (2012) Iron sparing and iron recycling contribute to increased superoxide dismutase capacity in iron starved Chlamydomonas. The Plant Cell 24:2649-2665. http://www.plantcell.org/content/24/6/2649 Blaby-Haas, C.E., Merchant, S.S. (2012) The ins and outs of algal metal transporters. Biochim. Biophys. Acta 1823:1531-1552. http://ac.els-cdn.com/S0167488912001012/1-s2.0-S0167488912001012- main.pdf?_tid=174199dc-1e02-11e2-a308- 00000aacb361&acdnat=1351100690_67232c936b82ce4cc753220eb2061b82 Urzica, E.I., Casero, D., Yamasaki, H., Hsieh, S.I., Adler, L.N., Karpowicz, S.J., Blaby-Haas, C.E., Clarke, S.G., Loo, J.A., Pellegrini, M., Merchant, S.S. (2012) Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. The Plant Cell 24:3921-48. http://www.plantcell.org/content/24/10/3921 Hsieh, S.I., Castruita, M., Malasarn, D., Urzica, E.I., Erde, J., Page, M.D., Yamasaki, H., Casero, D., Pellegrini, M., Merchant, S.S., Loo, J.A. (2012) The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. Mol Cell Proteomics 12:65-86. http://www.mcponline.org/content/12/1/65.full.pdf+html Blaby-Haas, C.E., Merchant, S.S. (2013) Iron sparing and recycling in a compartmentalized cell. Curr. Opin. Microbiol. 16:677-85. http://www.sciencedirect.com/science/article/pii/S1369527413001343 Gallaher, S.D., Fitz-Gibbon, S., Glaesener, A., Pellegrini, M., Merchant, S.S. (2015) Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies. The Plant Cell 27:2335-2352. http://www.plantcell.org/content/27/9/2335 Blaby-Haas, C.E., Merchant, S.S. (2017) Regulating trace metal economy in algae. Curr. Opin. Plant Biol. 39:88-96. doi: 10.1016/j.pbi.2017.06.005. https://reader.elsevier.com/reader/sd/pii/S1369526616302175?token=833D6EC78288573C96715F870 1D1903943B64E5D116C605F133FA5742237C0E8B34A04E1204870E7E3B557B62339AE25 Tsednee, M., Castruita, M., Salome, P.A., Sharma, A., Lewis, B.E., Schmollinger, S.R., Holbrook, K., Otegui, M., Khatua, K., Das, S., Datta, A., Chen, S., Ramon, C., Ralle, M., Weber, P.K., Stemmler, T.L., Pett- Ridge, J., Hoffman, B.M., Merchant, S.S. (2019) Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in manganese-deficient conditions. J. Biol. Chem. 294, 17626-17641. https://www.jbc.org/article/S0021-9258(20)30751-1/fulltext Schmollinger, S., Chen, S., Strenkert, D., Hui, C., Ralle, M., Merchant, S.S. (2021) Single-cell visualization and quantification of trace metals in Chlamydomonas lysosome related organelles. Proc. Natl. Acad. Sci USA, in press.
Synergistic Activities (up to five) 2011-2019 Member, Technical Advisory Committee on Algal Biofuels, ExxonMobil 2013 co-Organizer, Banbury Conference on Redesigning Photosynthesis. 2015-2019 Editor-in-Chief, The Plant Cell. 2016-2022 Member, GRC Conference Evaluation Committee 2020-present Chair, Center of Excellence for Plant and Microbial Science (joint venture John Innes Center and Chinese Academy of Science), Board
Identification of Possible Conflicts of Interest or Bias in Selection of Reviewers: Collaborators and Co-editors (last 48 months) Cynthia Amstutz (University of California, Berkeley), Daniele Armaleo (Duke University), Gilles Basset (University of Florida, Gainesville), Ralph Bock (Max Planck Institute – Molecular Plant Physiology, Potsdam, DE), Shawn Cokus (University of California, Los Angeles), Roberta Croce (Vrije University of Amsterdam, NL), Deqiang Duanmu (Huazhong Agricultural University, Wuhan, Hubei, CN), Benjamin Engel (Helmholtz Zentrum München, DE), Sorel Fitz-Gibbon (University of California, Los Angeles), Igor Grigoriev (DOE Joint Genome Institute), Arthur Grossman (Carnegie Institution of Science), Michael Hippler (Westfälische Wilhelms-Universität Münster, DE), Masa Iwai (Lawrence Berkeley National Laboratory), Tim Jeffers (University of California, Berkeley), Martin Jonikas (Princeton University), David Kramer (Michigan State University), Siavash Kurdistani (University of California, Los Angeles), J. Clark Lagarias (University of California, Davis), Carolyn Larabell (Lawrence Berkeley National Laboratory), Mary Lipton (Pacific Northwest National Laboratory), Joseph Loo (University of California, Los Angeles), Feng Ma (University of California, Los Angeles), Alizee Malnoe (Umea University, SE), Tabea Mettler-Altmann (Heinrich-Heine University, Düsseldorf, DE), Juliane Neupert (Max Planck Institute – Molecular Plant Physiology, Potsdam, DE), Carrie Nicora (Pacific Northwest National Laboratory), Krishna Niyogi (University of California, Berkeley), Trent Northern (Lawrence Berkeley National Laboratory), Matteo Pellegrini (University of California, Los Angeles), Jennifer Pett-Ridge (Lawrence Livermore National Laboratory), Sam Purvine (Pacific Northwest National Laboratory), Martina Ralle (Oregon Health & Science University), Silvia Ramundo (University of California, San Francisco), Jean-David Rochaix (University of Geneva, CH/Chinese Academy of Sciences, Shanghai, CN), Melissa Roth (University of California, Berkeley), Michael Schroda (Technische Universität Kaiserslautern, DE), Jeremy Schmutz (HudsonAlpha Institute for Biotechnology/DOE Joint Genome Institute), Eric Skaar (Vanderbilt University), Alison Smith (University of Cambridge), Timothy Stemmler (Wayne State University), Steven Theg (University of California, Davis), James Umen (Donald Danforth Plant Science Center), Olivier Vallon (Centre National de la Recherche Scientifique, Paris, FR), Setsuko Wakao (University of California, Berkeley/ Lawrence Berkeley National Laboratory), Daniel Westcott (University of California, Berkeley), Jennifer Wisecaver (Purdue University) Graduate and Postdoctoral Advisors not applicable (retired and deceased) Graduate and Postdoctoral Advisees (who remain research active in academic environment) Ian Blaby (DOE Joint Genome Institute), Crysten Blaby-Haas (Brookhaven National Laboratory), Nanette Boyle (Colorado School of Mines), Madeli Castruita (University of California, Los Angeles), Jen-Chih Chen (National Taiwan University, Taipei, TW.), Rory Craig (University of Edinburgh), Lital Davidi (University of California, Los Angeles), Rikard Fristedt (Chalmers University of Technology, Gothenburg, SE), Sean Gallaher (University of California, Los Angeles), Anne Glaesener (University of California, Berkeley), Patrice Hamel (Ohio State University), Anja Hemschemeier (Ruhr Universität, Bochum, DE), Kent Hill (University of California, Los Angeles), Kristen Holbrook (Amgen Inc.), Anne Hong-Hermesdorf (University of California, Los Angeles), Colleen Hui (University of California, Los Angeles/ Lawrence Livermore National Laboratory), Sharon La Fontaine (Deakin University), Hong Hua Li (Stanford University), Marcus Miethke (Helmholtz Institute for Pharmaceutical Research Saarland, DE), Jeffrey Moseley (University of California, Berkeley), Stacie Nakamoto (University of California, Los Angeles), Patrice Salome (Plant Editors, Peridot Scientific Communications), Stefan Schmollinger (University of California, Los Angeles), Frederik Sommer (Technische Universität Kaiserslautern, DE), Daniela Strenkert (University of California, Los Angeles), Muugii Tsednee (University of Tokyo, JP), Eugen Urzica (Westfälische Wilhelms-Universität Münster, DE), Anna Vitlin (University of California, Los Angeles), Hiroaki Yamasaki (Nagoya University, JP)
BIOGRAPHICAL SKETCH – KRISHNA K. NIYOGI
Education and Training The Johns Hopkins University, Baltimore, MD Biology B.A. 1986 University of Cambridge, Cambridge, UK Biochemistry M.Phil. 1988 Massachusetts Institute of Technology, Cambridge, MA Biology Ph.D. 1993 Carnegie Institution of Washington, Stanford Univ., Stanford, CA Plant Biology Postdoc 1993-97
Professional Experience Present 2017–present Investigator, Howard Hughes Medical Institute. 2006–present Professor, Department of Plant and Microbial Biology, University of California, Berkeley. 1999–present Faculty Scientist, Molecular Biophysics and Integrated Bioimaging Division, Bioenergetics Department, Lawrence Berkeley National Laboratory, Berkeley, CA. Previous 1997–2001 Assistant Professor, Department of Plant and Microbial Biology, University of California, Berkeley. 2001–2006 Associate Professor, Department of Plant and Microbial Biology, University of California, Berkeley. 2007 Visiting Professor, Department of Pharmaceutical Chemistry, UCSF. 2011–present Investigator, Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation. 2014–2015 Associate Chair, Department of Plant and Microbial Biology, University of California, Berkeley. 2015–2017 Chair, Department of Plant and Microbial Biology, University of California, Berkeley.
Publications (10 most closely related to the proposed project) Wakao S, Chin BL, Ledford HK, Dent RM, Casero D, Merchant SS, Pellegrini M, Niyogi KK (2014). Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. eLife 3: e02286. https://elifesciences.org/articles/02286 Dent RM, Sharifi MN, Haglund C, Malnoë, A, Calderon RH, Wakao S, Niyogi KK (2015). Large-scale insertional mutagenesis of Chlamydomonas supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetate-requiring mutants. Plant J 82: 337-351. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12806 Li Z, Peers G, Dent RM, Bai Y, Yang SY, Apel W, Leonelli L, Niyogi KK (2016). Evolution of an atypical de-epoxidase for photoprotection in the green lineage. Nature Plants 2:16140. https://www.nature.com/articles/nplants2016140 Ballottari M, Truong TB, De Re E, Erickson E, Stella GR, Fleming GR, Bassi R, Niyogi KK (2016). Identification of pH- sensing sites in the light harvesting complex stress-related 3 protein essential for triggering non-photochemical quenching in Chlamydomonas reinhardtii. J Biol Chem 291: 7334-7346. http://www.jbc.org/content/291/14/7334.long Roth MS, Cokus SJ, Gallaher SD, Walter A, Lopez D, Erickson E, Endelman B, Westcott D, Larabell C, Merchant SS, Pellegrini M, Niyogi KK (2017). Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production. Proc Natl Acad Sci USA 114: E4296-E4305. https://www.pnas.org/content/114/21/E4296.long Iwai M, Roth MS, Niyogi KK (2018). Subdiffraction-resolution live-cell imaging for visualizing thylakoid membranes. Plant J 96: 233-243. https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14021 Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Faflonker F, Bowen BP, Ataii NN, Song J, Chen J-H, Blaby-Haas CE, Larabell C, Auer M, Northen T, Merchant SS, Niyogi KK (2019). Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis. Plant Cell 31: 579-601. http://www.plantcell.org/content/31/3/579 García-Cerdán JG, Furst AL, McDonald KL, Schünemann D, Francis MB, Niyogi KK (2019). A thylakoid membrane- bound and redox-active rubredoxin (RBD1) functions in de novo assembly and repair of photosystem II. Proc Natl Acad Sci USA 116: 16631-16640. https://www.pnas.org/content/116/33/16631.long Gabilly ST, Baker CR, Wakao S, Crisanto T, Guan K, Bi K, Guiet E, Guadagno CR, Niyogi KK (2019). Regulation of photoprotection gene expression in Chlamydomonas by a putative E3 ubiquitin ligase complex and a homolog of CONSTANS. Proc Natl Acad Sci USA 116: 17556-17562. https://www.pnas.org/content/116/35/17556.long García-Cerdán JG, Schmid EM, Takeuchi T, McRae I, McDonald K, Yordduangjun N, Hassan AM, Grob P, Xu CS, Hess HF, Fletcher DA, Nogales E, Niyogi KK (2020). Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and promotes carotenoid accumulation in Chlamydomonas. Proc Natl Acad Sci USA 117: 12452-12463. https://www.pnas.org/content/117/22/12452.long
Synergistic Activities (up to five) 2006-2014 Member, Scientific Advisory Board, Aurora Algae, Inc. 2010–2016 Area Representative, International Society of Photosynthesis Research. 2011 Chair, Gordon Research Conference on Photosynthesis. 2014 Organizer, 16th International Conference on the Cell and Molecular Biology of Chlamydomonas. 2017-present Editorial Board, Proceedings of the National Academy of Sciences of the USA.
Identification of Possible Conflicts of Interest or Bias in Selection of Reviewers: Collaborators and Co-editors (last 48 months) William Adams (Univ. of Colorado), Nanette Boyle (Colorado School of Mines), Crysten Blaby-Haas (BNL), Carlos Bustamante (UCB), Luca Dall’Osto (Univ. of Verona), Barbara Demmig-Adams (Univ. of Colorado), Adam Deutschbauer (LBNL), Tim Donohue (Univ. of Wisconsin), Graham Fleming (UCB), Dan Fletcher (UCB), Matt Francis (UCB), Hernan Garcia (UCB), Katarzyna Glowacka (Univ. of Nebraska), Michel Havaux (CEA-Cadarache), Harald Hess (Janelia), Martin Jonikas (Princeton), Johannes Kromdijk (Univ. of Cambridge), Carolyn Larabell (UCSF), Andrew Leakey (Illinois), Peggy Lemaux (UCB), Mary Lipton (PNNL), Martin Lohr (Mainz), Steve Long (Illinois), Yandu Lu (Hainan Univ.), Anastasios Melis (UCB), Sabeeha Merchant (UCB), Brent Mishler (UCB), Elena Monte (CRAG, Barcelona), Tomas Morosinotto (Univ. of Padua), Eva Nogales (UCB), Trent Northen (LBNL), Don Ort (Illinois), Matteo Pellegrini (UCLA), Gilles Peltier (CEA-Cadarache), Elizabeth Purdom (UCB), Danja Schünemann (Ruhr University Bochum), Brian Staskawicz (UCB), Hiroko Takahashi (Saitama Univ.), Peter Jomo Walla (Technische Universität Braunschweig), Chia-Lin Wei (Jackson Lab), Francis-André Wollman (IBPC). Graduate and Postdoctoral Advisors Gerald R. Fink (Whitehead Institute, MIT), Olle Björkman (Carnegie Institution), Arthur R. Grossman (Carnegie Institution) Graduate and Postdoctoral Advisees Simon Alamos (UCB), Cindy Amstutz (Sound Agriculture), Johan Andersen-Ranberg (Copenhagen), Ute Armbruster (MPI-Golm), Mohammad Anwaruzzaman (Bayer), Tom Avenson, Yong Bai (CA Dept. of Public Health), Chris Baker (HHMI), Irene Baroli (Univ. of Buenos Aires), Gabriella Benko (UCB), Vincent Boudreau (UCB), Ethan Boynton (UCB), Matthew Brooks (USDA-ARS), Adrien Burlacot (HHMI), Robert Calderon (Umeå), Shih-Wei Chuang (UCB), Thien Crisanto (UCB), Oliver Dautermann (BASF), Rachel Dent, Ben Endelman (Pairwise), Erika Erickson (NREL), Beat Fischer (Switzerland), Stéphane Gabilly (France), Olga Gaidarenko (HHMI), José Garcia-Cerdán (Colorado), Chris Gee (JBEI), Talila Golan, Benjamin Gutman (Union of Concerned Scientists), Miehie Han (Seoul National Univ.), Alex Hertle (MPI- Golm), Masakazu Iwai (LBNL), Tim Jeffers (UCB), Jeff Johnson, Hou-Sung Jung (CHOP), Heidi Ledford (Nature), Laurie Leonelli (Illinois), Xiao-Ping Li (Rutgers), Zhirong Li (CA Dept. of Public Health), Dagmar Lyska (Duesseldorf), Alizée Malnoë (Umeå), Nina Maryn (UCB), Patricia Müller-Moulé (UC-Davis), Dhruv Patel (UCB), Graham Peers (Colorado State), Melissa Roth (UCB), Patrick Shih (UC-Davis), Jai Shin (Johns Hopkins), Anchalee Sirikhachornkit (Kasetsart Univ.), Phoi Tran (CA Dept. of Public Health), Jernej Turnsek (HHMI), Thuy Truong (Xencor), Setsuko Wakao (LBNL), Daniel Westcott (Climax Foods).
CURRICULUM VITAE Professor Dr. Ralph Bock
Date of Birth: October 8, 1967 (Wolfen, Germany) Nationality: German
Education and positions held 1988-1993: Study of Biology, University of Halle, Germany 1993: MSc (Diploma) in Genetics (Grade: "Excellent"), Institute of Genetics, University of Halle, Germany (Supervisor: Prof. Dr. Rudolf Hagemann) 1993-1996: PhD work at Waksman Institute, Rutgers, The State University of New Jersey, USA, and Institute for Biology III, University of Freiburg, Germany July 1996: PhD in Genetics (Grade: "summa cum laude"), University of Freiburg; Title: In vivo analyses on RNA editing in higher plant plastids (Supervisor: Prof. Dr. Hans Kössel) 1996-2001: Assistant Professor, Institute for Biology III, University of Freiburg 1999: Habilitation (venia legendi) for Genetics and Molecular Biology 2001: Appointed as Full Professor (C4) and Chair of Biochemistry and Plant Biotechnology at the Westfälische Wilhelms University of Münster, Germany 2001-2004: Director of the Institute of Biochemistry and Plant Biotechnology, University of Münster since 2004: Director, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, and Professor of Biological Sciences, Department of Biology, University of Potsdam, Germany
Selected academic awards and distinctions 1993-1996: Research fellowship of the Boehringer Ingelheim Fonds 1996: Dissertation Prize of the German Genetic Society 1997: Hans Spemann Prize of the University of Freiburg 2017: Martin Gibbs Medal of the American Society of Plant Biologists (ASPB) since 2010: Elected Member of the National Academy of Science (Leopoldina) since 2011: Adjunct Professor, NiBio, Norwegian Institute of Bioeconomy Research, Norway since 2015: Elected Member of EMBO (European Molecular Biology Organization) since 2016: Honorary Professor, Hubei University, Wuhan, China since 2017: Distinguished Professor, Hubei University, Wuhan, China since 2021: Elected Member of the Berlin-Brandenburg Academy of Sciences and Humanities (BBAW) ERC Advanced Grant (2.5 million €, 2015-2021) Highly Cited Researcher (Web of Science, Thomson Reuters, Clarivate Analytics) >240 peer-reviewed publications; H-index (Google Scholar): 81; >21,500 citations
Scientific community service Organization of international conferences (selection): 2005: Chair of the 1st International conference on "Plant-based vaccines and antibodies", Prague, Czech Republic 2012: Co-Organizer of the 15th International Chlamydomonas Conference, Potsdam, Germany 2013: Vice Chair of the 3rd International Symposium on Chloroplast Genomics and Genetic Engineering (ISCGGE), New Brunswick, USA 2015: Vice Chair of the Gordon Research Conference on “Chloroplast biotechnology”, Ventura, USA 2017: Chair of the Gordon Research Conference on “Chloroplast biotechnology”, Ventura, USA Advisory boards, selected committees and panels (selection): European Food Safety Authority (EFSA): Scientific expert in the Working Group “Guidelines for the assessment of genetically modified plants used as production platform for non-food/feed products” (2005-2009) Scientific Advisory Board of the CNRS Institute in Strasbourg, France (Institut de Biologie Moleculaire des Plantes, IBMP): Member (2007-2014), Chair (2011) Scientific Advisory Board of the Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany: Vice Chair (2007-2015) European Academies Science Advisory Council (EASAC): Member of the Working Group on “GM crops” (2012- 2013) Plant Science Review Panel of the DFG (National Science Foundation, Germany): Member (2012-2020) DFG Senate Commission on Genetic Research: Member (since 2017) Member of the steering committee of the Section “Organismal and Evolutionary Biology” of the National Academy of Science (since 2018) Member of the Conference Evaluation Committee (CEC) of the Gordon Research Conferences (since 2018) Member of the Working Group on “Regulation of genome-edited plants” of the National Academy of Science (2018-2020) Activities with scientific journals: Editor, Current Genetics (2005-2014); Associate Editor, Transgenic Research (2006-2020); Consulting Editor, Advances in Photosynthesis and Respiration (2009-2015); Editorial Board, Eukaryotic Cell (2010-2012); Editorial Board, Plant Biotechnology Journal (since 2013); Senior Editor, Plant Cell (since 2015); Guest Editor, Annual Reviews of Plant Biology (2017-2018); Associate Editor, Molecular Plant (since 2017)
Research interests - Plastid genetics and molecular biology: transcriptional and post-transcriptional regulation of gene expression, chloroplast RNA metabolism, RNA editing, reverse genetics, plastid-nuclear interaction, organelle inheritance - Photosynthesis: regulation of photosynthesis, assembly of protein complexes in thylakoid membranes - Biotechnology and synthetic biology: organelle transformation, inducible gene expression, molecular farming, metabolic engineering, resistance engineering, genome editing - Evolutionary biology: experimental evolution, gene transfer between organelles and the nucleus, horizontal gene transfer - Systems biology and gene expression in the green algal model Chlamydomonas and the red algal model Porphyridium
5 selected publications relevant to the proposal Neupert, J., Karcher, D. and Bock, R. (2009). Generation of Chlamydomonas strains that efficiently express nuclear transgenes. Plant J., 57, 1140-1150. Shao, N., Duan, G. Y. and Bock, R. (2013). A mediator of singlet oxygen responses in Chlamydomonas reinhardtii and Arabidopsis identified by a luciferase-based genetic screen in algal cells. Plant Cell, 25, 4209– 4226. Barahimipour, R., Strenkert, D., Neupert, J., Schroda, M., Merchant, S. S. and Bock, R. (2015). Dissecting the contributions of GC content and codon usage to gene expression in the model alga Chlamydomonas reinhardtii. Plant J., 84, 704-717. Li, Z. and Bock, R. (2018). Replication of bacterial plasmids in the nucleus of the red alga Porphyridium purpureum. Nature Commun., 9, 3451. Neupert, J., Gallaher, S. D., Lu, Y., Strenkert, D., Segal, N., Barahimipour, R., Fitz-Gibbon, S. T., Schroda, M., Merchant, S. S. and Bock, R. (2020). An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas. Nature Commun., 11, 6269. 5 other selected publications Stegemann, S. and Bock, R. (2009). Exchange of genetic material between cells in plant tissue grafts. Science, 324, 649-651. Fuentes, I., Stegemann, S., Golczyk, H., Karcher, D. and Bock, R. (2014). Horizontal genome transfer as an asexual path to the formation of new species. Nature, 511, 232-235. Zhang, J., Khan, S. A., Hasse, C., Ruf, S., Heckel, D. G. and Bock, R. (2015). Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids. Science, 247, 991-994. Ruf, S., Forner, J., Hasse, C., Kroop, X., Seeger, S., Schollbach, L., Schadach, A. and Bock, R. (2019). High- efficiency generation of fertile transplastomic Arabidopsis plants. Nature Plants, 5, 282-289. Wu, G.-Z., Meyer, E. H., Richter, A., Schuster, M., Ling, Q., Schöttler, M. A., Walther, D., Zoschke, R., Grimm, B., Jarvis, P. and Bock, R. (2019). Control of retrograde signaling by protein import and cytosolic folding stress. Nature Plants, 5, 525-538.
BIOGRAPHICAL SKETCH – SUSAN K. DUTCHER (5/2021)
Education and Training Colorado College Biology B.A. 1974 University of Washington Genetics Ph.D. 1975- 1980 Rockefeller University Cell Biology post-doc 1980- 1983 Research and Professional Experience
Present 1999-present Professor, Department of Genetics Washington University in St Louis
Previous 2016 - 2018 Interim Director, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
2006 - 2009 Interim Chair, Department of Genetics, Washington University School of Medicine, St. Louis, MO
1983 -1999 Assistant to Full Professor, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder
1983 -1984 Adjunct Assistant Professor, The Rockefeller University, New York City
Publications (10 most closely related to the proposed project)
1. Li, J.B., Gerdes, J.M., Haycraft, C.J., Fan, Y., Teslovich, T.M., May-Simera, H., Li, H., Blacque, O., Li, L., Leitch, C.C., Lewis, R.A., Green, J.S., Parfrey, P.S., Leroux, M.R., Davidson, W.S., Beales, P.L., Guay-Woodford, L.M., Yoder, B.K., Stormo, G.D., Katsanis, N. and Dutcher, S.K. (2004). Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell 117, 541-552. https://pubmed.ncbi.nlm.nih.gov/15137946/
2. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P-F, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S-i, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu S-H, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano, RS, Boore, JL (2008). The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69. https://pubmed.ncbi.nlm.nih.gov/18079367/
3. Kwan, A. Kulp, D., Dutcher, S.K., and Stormo, G.D. (2009). Improving Gene-finding in Chlamydomonas reinhardtii: GreenGenie2. BMC Genomics, 10: e210. https://pubmed.ncbi.nlm.nih.gov/19422688/
4. Lin, H., Kwan, A. L., and Dutcher, S. K. (2010). Synthesizing and Salvaging NAD+: Lessons Learned from Chlamydomonas reinhardtii. PLoS Genetics 6: e100-105. PMCID: PMC3784568. https://pubmed.ncbi.nlm.nih.gov/20838591/
5. Albee, A. J., Kwan, A.L., Lin, H., Granas, D., Stormo, G. D., and Dutcher, S.K. (2013). Whole genome transcriptome analysis of Chlamydomonas reinhardtii identifies new cilia genes that affect cell cycle progression. G3, 3: 979-91. PMCID: PMC3689809. https://pubmed.ncbi.nlm.nih.gov/23604077/
6. Lin, H. Zhang, Z., Guo, S., Chen, F., Kessler, J.M., Wang, Y.M., and Dutcher, S.K. (2015). A NIMA- related kinase suppresses the flagellar instability associated with the loss of multiple axonemal structures. PLoS Genet. 11: e1005508. https://pubmed.ncbi.nlm.nih.gov/26348919/
7. Audano, P.A., Graves-Lindsay, T.A., Cantsilieris, S., Sorensen, M., Welch, A.E., Nelson, B.J., Dougherty, M.L., Dutcher, S.K., Warren, W. C., Wilson, R.K., and Eichler, E.E. (2019). Characterizing the major structural variant alleles of the human genome. Mol. Cell. 176, 663-675. https://pubmed.ncbi.nlm.nih.gov/30661756/
8. Pandey, M., Stormo, G.D., and Dutcher, S.K. (2020). Alternative Splicing during the Chlamydomonas reinhardtii Cell Cycle. G3, Oct 5;10(10):3797-3810. doi: 10.1534/g3.120.401622. PMID: 32817123; PMCID: PMC75334427. https://academic.oup.com/g3journal/article/10/10/3797/6053570
9. Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S; NHGRI Centers for Common Disease Genomics, Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. (2020) Mapping and characterization of structural variation in 17,795 human genomes. Nature. 583(7814):83-89. Epub 2020/05/28. doi: 10.1038/s41586- 020-2371-0. PMID: 32460305; PMCID: PMC7547914. https://pubmed.ncbi.nlm.nih.gov/32460305/
10. Gui, M. Ma, M, Sze-Tu, E., Wang, X., Koh, Zhong, E., Berger, B., Davis, J., Dutcher, S.K., Zhang, R. and Brown, A. (2021). Structures of radial spokes and associated complexes important for ciliary motility, Nature Structural and Molecular Biology Jan;28(1):29-37. doi: 10.1038/s41594-020-00530-0. Epub 2020 Dec 14. PMID: 33318703. https://pubmed.ncbi.nlm.nih.gov/33318703/
Honors and Awards
2004, William Trager Memorial Award for Outstanding Paper of the Year, Society of Protozoologists 2010, Elected Fellow, American Academy of Arts and Sciences 2017, Washington University Distinguished Faculty Award for Mentoring of Junior Faculty 2017, Elected Fellow, American Society of Cell Biology 2017, Elected Fellow, American Association for the Advancement of Science 2018, Washington University Distinguished Investigator Award
Synergistic Activities (up to five) 2004-present Associate Editor, PLoS Genetics 2006 Organizer, 12th International Meeting on Cell and Molecular Biology of Chlamydomonas 2007-2009 Member, Council of American Society of Cell Biology 2008, 2011, 2017 Co-organizer, EMBO Conference on Centrosomes and Spindle Pole Bodies 2019-2022 Member, Council of American Association for the Advancement of Science
Identification of Possible Conflicts of Interest or Bias in Selection of Reviewers:
Goncales Abecasis (Regeneron, NY), Phil Bayly (Washington University), Michael Boehnke (University of Michigan), Alan Brown (Harvard), Don Conrad (Oregon Health and Sciences, Portland), Evan Eichler (University of Washington), Nelson Freimer (UCLA), Fanni Gergely (Cancer Institute, Cambridge, UK), Ira Hall (Yale University), David Haussler (University of California, Santa Cruz), Kaiyao Huang (Chinese Academy of Sciences), Stephen King (University of Connecticut), Adam Locke (Regeneron, NY), Eric Lander (MIT/Broad Institute), Takashi Ochi (Leeds University, UK), Heymut Omran (University of Muenster, DE), Winfield Sale (Emory University), Michael Schroda (Technische Universität Kaiserslautern, DE), Valerie Schneider (NLM/NIH), Jay Shendure (University of Washington), Nathan Stitizel (Washington University in St Louis), Gary Stormo (Washington University), Ting Wang (Washington University in St Louis), James Umen (Danforth Plant Science Center), Mark van Breugel (MRC, Cambridge, UK), Richard Wilson (University of Ohio, National Children’s Hospital) , Mike Zody (New York Genome Center)
Graduate and Postdoctoral Advisors not applicable (retired and deceased)
Graduate and Postdoctoral Advisees (who remain research active in academic environment) Haley Abel (Washington University), Lea Alford (Oglethorpe University, GA), Mathieu Bottier (Univeristy of Dundee, UK), Miao Gui (Harvard University), Stephen J King, (University of Florida), Billy Jin Li (Stanford University), Maureen Wirschell (Danforth Plant Sciences Center), Ryosuke Yamamoto (Osaka University)
Current Research Funding
Agency Dates Title PI 09/28/2016- 10/31/2021 Characterizing Dynamic Transitions and Bifurcations to Co-PI with P. Bayly NSF Understand How Flagella Beat
NIH 7/12019-6/30/2024 Genetic Analysis of Centrioles and Cilia PI (NIGMS) Multi-PI NIH Regulation of Motile Cilia Assembly in Lung Disease 2/2020-1/2024 with S. Brody and M. (NHLBI) (Renewal) Mahjoub
CV Crysten Blaby-Haas
Name Title Crysten Blaby Biologist
Education 2006 – 2011 Ph.D. University of Florida in Microbiology and Cell Science 2002 – 2006 B.S. University of Florida in Microbiology and Cell Science with a minor in Chemistry
Professional Experience 2020 – present Biologist, Brookhaven National Laboratory 2017 – present Adjunct Professor, Stony Brook University 2017 – present Laboratory Research Manager, Quantitative Plant Science Initiative 2017 – 2020 Associate Biologist, Brookhaven National Laboratory 2015 – 2017 Assistant Biologist, Brookhaven National Laboratory 2011 – 2015 NIH NRSA Postdoctoral Fellowship, University of California, Los Angeles
Selected Publications (* = equal contribution; full list available on Google Scholar: https://scholar.google.com/citations?user=3wJ7hBwAAAAJ&hl=en&oi=ao) Blaby-Haas CE. (2021) Cyanobacteria provide a new paradigm in the regulation of cofactor dependence. Proc Natl Acad Sci USA 118 (7) e2100281118. PMID: 33547093 Cole B, Bergmann D, Blaby-Haas CE, …Dickel D. (2021) Plant Single-Cell Solutions for Energy and the Environment. Comm Biol under review . Foflonker F and Blaby-Haas CE. (2021) Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function discovery. Mol Biol Evol 38(2): 650-662. PMID: 32886760 Gallaher S, Craig R, Ganesan I, Purvine S, McCorkle SR, Grimwood J, Strenkert D, Davidi L, Roth MS, Jeffers TL, Lipton M, Niyogi KK, Schmutz J, Theg SM, Blaby-Haas CE, Merchant SS. Polycistronic gene expression is widespread in the green algal lineage. Proc Natl Acad Sci USA 118 (7) e2017714118 Grosjean N and Blaby-Haas CE. (2020) Leveraging computational genomics to understand the molecular basis of metal homeostasis. Invited Tansley Review, New Phytol 228(5): 1472-1489. PMID: 32696981 Marckmann D, Trasnea P, Schimpf J, Winterstein C, Andrei A, Schmollinger S, Blaby-Haas CE, Friedrich T, Daldal F, Koch H. (2019) The cbb3-type cytochrome oxidase assembly factor CcoG is a widely distributed novel cupric reductase. Proc Natl Acad Sci USA 116 (42): 21166-21175. PMID: 31570589 Blaby-Haas CE and Merchant SS. (2019) Comparative and Functional Algal Genomics. Ann Rev Plant Biol 70: 605- 638. PMID: 30822111 Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen J, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SM, Niyogi KK. (2019) A molecular switch for oxygenic photosynthesis and metabolism in a green alga. Plant Cell 31(3): 579-601. PMID: 30787178 Blaby IK and Blaby-Haas CE. (2017) Genomics and functional genomics in Chlamydomonas reinhardtii. In Chlamydomonas: Molecular Genetics and Physiology, pp. 1-26. Springer, Cham. Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, ... and Prochnik S. (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA 17: 201703088. PMC5547612 Fristedt R, Herdean A, Blaby-Haas CE, Mamedov F, Merchant SS, Last RL and Lundin B. (2015) PHOTOSYSTEM II PROTEIN33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem II supercomplexes in Arabidopsis. Plant Physiol 167(2): 481-92. PMC4326745 Blaby IK, Blaby-Haas CE, Tourasse N, Hom EF, Lopez D, Aksoy M, ... and Prochnik S. (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci 19: 672-680. PMC4185214 Blaby-Haas CE, Padilla-Benavides T, Stübe R, Argüello JM and Merchant SS. (2014) Evolution of a plant-specific copper chaperone family for chloroplast copper homeostasis. Proc Natl Acad Sci USA 111(50): E5480-E5487. PMC4273408 Glaesener AG, Merchant SS and Blaby-Haas CE. (2013) Iron economy in Chlamydomonas reinhardtii. Front Plant Sci 4:337. PMC3759009 Ming R, Vanburen R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, ... and Shen-Miller J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol 14(5): R41. PMC4053705 Blaby-Haas CE and Merchant SS. (2013) Sparing and salvaging metals in chloroplasts in Metals in Cells. V. Culotta and R.A. Scott eds. Encyclopedia of Inorganic and Bioinorganic Chemistry (EIBC), EIC Books Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas CE, Clarke SG, Loo JA, Pellegrini M, and Merchant SS. (2012) Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell 24(10): 3921-48. PMC3517228 Gerdes S, El Yacoubi B, Bailly M*, Blaby IK *, Blaby-Haas CE*, Jeanguenin L*, Lara-Núñez A*, Pribat A*, Waller JC*, Wilke, A *, Overbeek R, Hanson AD, and de Crécy-Lagard V. (2011) Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics 12 Suppl 1: S2. PMC3223725 Blaby-Haas CE and de Crécy-Lagard V. (2011) Mining high-throughput experimental data to link gene and function. Trends in Biotech, 29(4): 174-182. PMC3073767
Synergestic Activities PI: Quantitative Plant Science Initiative. DOE-BER SFA (2020 – present) PI: Managing the cellular zinc economy: proteomics-enabled predictive understanding of zinc hierarchy (EMSL user project, starts 2020) co-PI: Laboratory Directed Research and Development Program (LDRD), “Laying the Foundation for an Integrated Center for Sequence-to-Function Discovery”, 2021 – 2024, (PI: Lin Yang, National Synchrotron Light Source II) co-PI: Gene function discovery in photosynthesis: A multi-omics approach (FICUS, JGI-EMSL CSP, starts 2020, PI: Sabeeha Merchant, University of California, Berkeley) co-PI: Systems Analysis of Trophic Transitions in Chromochloris zofingiensis, an Emerging Model Green Alga with Promising Biofuel Potential (DOE BER, Biosystems Design, 2017 – 2022, PI: Krishna Niyogi, University of California, Berkeley) co-PI: Sequence to function: integrative high-throughput approaches for functional prospecting in photosynthetic organisms (JGI Synthetic Biology CSP, initiated 2017, PI: Ian K. Blaby, Joint Genome Institute, Lawrence Berkeley Laboratory) co-PI: Systems Analysis of Trophic Transitions in Chromochloris zofingiensis, an Emerging Model Green Alga with Promising Biofuel Potential (FICUS, JGI-EMSL CSP, initiated 2017, PI: Krishna Niyogi, University of California, Berkeley) co-PI: Open Green Genomes (JGI Synthetic Biology CSP, initiated 2017, PI: James Leebens-Mack, University of Georgia)
Personal details Gender Male Name and first name: SCHRODA Michael Country Germany Current position Function Full professor Appointment(s) in research/teaching organisation(s) Organisation Department Laboratory Postcode Town TU Faculty of Molecular Biotechnology & 67663 Kaiserslautern Kaiserslautern Biology Systems Biology Other public or private organisation(s) Organisation Position Town Country
Previous positions Start date End date Town Organisation Function 1994 1999 Freiburg, DE University of Freiburg, Biology III PhD student 1999 2001 Paris, FR CNRS, Institut de Biologie Physico-Chimique Post-doc 2001 2003 Freiburg, DE University of Freiburg, Biology II Staff scientist 2003 2008 Freiburg, DE University of Freiburg, Biology II Junior professor 2008 2011 Potsdam, DE MPI for Molecular Plant Physiology Group leader 2011 - Kaiserslautern, DE TU Kaiserslautern Full professor Career interruption(s)
Education Diploma in Biology, University of Marburg/University of Tennessee, Knoxville/University of Helsinki, 1994 PhD in Molecular Genetics, University of Freiburg, 1999 Habilitation, University of Freiburg, 2007 Scientific products Grants, prizes, awards, fellowships, etc. 1990-1994 Scholar of the Friedrich-Ebert-Stiftung 1999-2001 DAAD Postdoctoral Fellowship 2001 Hans-Grisebach-Prize of the Faculty of Biology, University of Freiburg for outstanding thesis
Federal state of Baden-Württemberg grant for Junior professors Three individual DFG grants Member of the DFG research group FOR304 “Gene Expression and Proteome Dynamic in Chlamydomonas reinhardtii” Member of the GoFORSYS consortium "Photosynthesis and Growth: A Systems Biology-based Approach” Individual grant from the federal state of Rhineland-Palatinate Member of the DFG research group FOR2092 “Biogenesis of thylakoid membranes: spatiotemporal organization of photosynthetic protein complex assembly” Member of the DFG TRR175 “The Green Hub - Central Coordinator of Acclimation in Plants” Member of the DFG priority program 1927 “Fe-S for life” JGI Community Science Program “High-throughput sequencing and metabolomics enabled phenomics to investigate the integration of heat and circadian responses in the model green alga Chlamydomonas reinhardtii“ (with Ru Zhang)
81 publications in international peer-reviewed journals. H-index: 39 (Google Scholar) 5 publications most relevant to the proposal What is the major contribution of this publication? 1 Theis J, Lang J, Spaniol B, Ferte S, Niemeyer J, Sommer F, Zimmer This paper is on the functional characterization of a protease in the D, Venn B, Mehr SF, Muhlhaus T, Wollman FA, Schroda M (2019) chloroplast. It shows how valuable comparative quantitative shotgun The Chlamydomonas deg1c mutant accumulates proteins proteomics is to get hands on a mutant phenotype. These analyses involved in high light acclimation. Plant Physiol 181: 1480-1497 require a well-annotated genome. 2* Hemme D, Veyel D, Mühlhaus T, Sommer F, Juppner J, Unger AK, Here we used quantitative shotgun proteomics, metabolomics and Sandmann M, Fehrle I, Schönfelder S, Steup M, Geimer S, Kopka lipidomics to conduct a time-resolved analysis at several systems J, Giavalisco P, Schroda M (2014) Systems-wide analysis of levels on Chlamydomonas cells subjected to 24 h of heat stress. We acclimation responses to long-term heat stress and recovery in could reveal that the heat stress response consists of several the photosynthetic model organism Chlamydomonas reinhardtii. response modules that are temporally implemented in a highly Plant Cell 26: 4270-4297 coordinated manner. 3* Schmollinger S, Mühlhaus T, Boyle NR, Blaby IK, Casero D, A systems biology approach based on transcriptomics and Mettler T, Moseley JL, Kropat J, Sommer F, Strenkert D, Hemme quantitative proteomics to analyze the responses of Chlamydomonas D, Pellegrini M, Grossman AR, Stitt M, Schroda M, Merchant SS cells to nitrogen deprivation. Not possible without a well-annotated (2014) Nitrogen-sparing mechanisms in Chlamydomonas affect genome. the transcriptome, the proteome, and photosynthetic metabolism. Plant Cell 26: 1410-1435 4* Strenkert D, Schmollinger S, Sommer F, Schulz-Raffelt M, Schroda In this paper we used ChIP to analyze the regulation of gene M (2011) Transcription factor dependent chromatin remodeling expression at the chromatin level in response to heat stress and at heat shock and copper responsive promoters in copper deprivation. Chlamydomonas reinhardtii. Plant Cell 23: 2285-2301 5* Merchant, S. S., Prochnik, S. E., Vallon, ….., Grimwood, J., This is the founding paper of Chlamydomonas genomics. I Schmutz, J., Cardol, P., ……, Dutcher, S.,….., Hanikenne, M., ….. contributed with the annotation of ~100 genes, with a special focus Niyogi, K., ….., Schroda, M., …., Grigoriev, I. V., Rokhsar, D. S., and on molecular chaperones. Grossman, A. R. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245- 250 5 other publications of interest What is the major contribution of this publication? 6 Gupta TK, Klumpe S, Gries K, Heinz S, Wietrzynski W, Ohnishi N, This is a structure-function analysis of the VIPP1 protein based on Niemeyer J, Spaniol B, Schaffer M, Rast A, Ostermeier M, Strauss cryo-EM. In an extensive teamwork we could get a high-resolution M, Plitzko JM, Baumeister W, Rudack T, Sakamoto W, Nickelsen structure of cyanobacterial VIPP1 We could show that it forms large J, Schuller JM, Schroda M, Engel BD (2021) Structural basis for basket-like structures and could identify a novel nucleotide binding VIPP1 oligomerization and maintenance of thylakoid membrane site. Using CLEM we could identify VIPP1 in Chlamydomonas and integrity. Cell: in press demonstrate that it forms rods that can tubulate thylakoid membranes. They connect inner envelopes and thylakoids. 7 Crozet P, Navarro FJ, Willmund F, Mehrshahi P, Bakowski K, Here we teamed up with several groups to generate a Modular Lauersen KJ, Perez-Perez ME, Auroy P, Gorchs Rovira A, Sauret- Cloning toolbox consisting of 119 genetic parts for algal synthetic Gueto S, Niemeyer J, Spaniol B, Theis J, Trosch R, Westrich LD, biology. Up to seven parts can be assembled in a predefined order via Vavitsas K, Baier T, Hubner W, de Carpentier F, Cassarini M, Golden Gate cloning in a single reaction to generate transcriptional Danon A, Henri J, Marchand CH, de Mia M, Sarkissian K, units. These can be further assembled into multi-gene constructs in a Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda single reaction. M, Smith AG, Lemaire SD (2018) Birth of a photosynthetic chassis: a MoClo toolkit enabling synthetic biology in the microalga Chlamydomonas reinhardtii. ACS Synth Biol 7: 2074- 2086 8 Nordhues A, Schöttler MA, Unger AK, Geimer S, Schönfelder S, Here we employed amiRNA technology for the functional analysis of Schmollinger S, Rütgers M, Finazzi G, Soppa B, Sommer F, VIPP1 in Chlamydomonas. Its downregulation led to the appearance Mühlhaus T, Roach T, Krieger-Liszkay A, Lokstein H, Crespo JL, of aberrant structures at regions where multiple thylakoid membrane Schroda M (2012) Evidence for a role of VIPP1 in the structural layers converge and to dramatic thylakoid swelling in high light. These organization of the photosynthetic apparatus in phenotypes were reproduced in cyanobacteria in the Gupta 2021 Chlamydomonas. Plant Cell 24: 637-659 paper. 9 Mühlhaus T, Weiss J, Hemme D, Sommer F, Schroda M (2011) In this paper, we introduced 15N metabolic labeling to Quantitative shotgun proteomics using a uniform 15N-labeled Chlamydomonas and its use to get quantitative information on standard to monitor proteome dynamics in time course changes in the proteome during the first three hours of heat stress. experiments reveals new insights into the heat stress response of Not possible without a well-annotated genome. Chlamydomonas reinhardtii. Mol Cell Proteomics 10: M110 004739 10 Schroda M, Vallon O, Whitelegge JP, Beck CF, Wollman FA (2001) This paper characterizes the chloroplast GrpE-type nucleotide The chloroplastic GrpE homolog of Chlamydomonas: two exchange factor CGE1 in Chlamydomonas. We demonstrate that isoforms generated by differential splicing. Plant Cell 13: 2823- temperature-dependent alternative splicing gives rise to two 2839 different isoforms of the CGE1 protein. Other activities Executive board, supervision of students, teaching, memberships in panels or individual scientific reviewing activities… since 2020 member of the DFG evaluation panel 202, plant sciences 2019 member of the ANR evaluation board since 2018 SAB member of NordQAUA 2015-2018 dean of the Faculty of Biology, TU Kaiserslautern Since 2014 faculty board member, Faculty of Biology, TU Kaiserslautern since 2014 speaker of the Research Initiative BioComp (20 PIs), TU Kaiserslautern 2014-2017 associate editor J Phycology since 2011 trusted lecturer of the Friedrich-Ebert foundation
Reviewer of > 12 papers/year Supervisor of 14 PhD, 34 Master and 23 Bachelor students (obtained their degree in my group) iGEM supervisor since 2019 (our team was 3rd in 2019) Teacher for Molecular Biotechnology at Bachelor’s level (~40 lectures, practical class for ~120 students per year) Teacher for Systems Biology, Synthetic Biology and plant acclimation at Master’s level (~20 lectures, practical classes for ~30 students/year) Research interests Please briefly describe your research activities over the last 10 years My main interest is to understand how protein homeostasis is maintained in a plant cell. For this, we are functionally characterizing the components responsible, i.e., molecular chaperones and proteases. Moreover, we are investigating the signaling pathways involved in the cytosol leading to the activation of HSF1, and in the activation of a subset of genes when protein homeostasis is disturbed in the chloroplast. I am interested in analyzing the components involved in the biogenesis of thylakoid membranes and the protein complexes therein. A special focus lies here on PSII, whose repair cycle is also subject of our research. I am continuously developing methodology for mass spectrometry-based proteomics. A focus lies on methods for the analysis of protein-protein interactions, the absolute quantification of target proteins, and the analysis of changes in the proteome over time. Since many years I have been developing tools for the expression of transgenes in Chlamydomonas. With the MoClo strategy this has become routine in our hands and we are getting more and more engaged in algal synthetic biology. My new hobby here is to supervise an iGEM team every year where I get the students to work with the MoClo strategy.
Professor Alison G Smith Department of Plant Sciences, University of Cambridge, UK URL: https://www.plantsci.cam.ac.uk/research/alisonsmith Email: [email protected]
EDUCATION
1981 PhD in Biochemistry – University of Cambridge 1978 MPhil in Biochemistry – University of Cambridge 1977 BSc in Biochemistry (1st class) – University of Bristol
APPOINTMENTS AND POSTS HELD
2017- date Head of Dept, Plant Sciences, University of Cambridge 2014-2015 Acting Head of Dept, Plant Sciences, University of Cambridge 2007- date Professor of Plant Biochemistry, University of Cambridge 2001-2007 Reader in Plant Metabolism, University of Cambridge 1989-2001 University Lecturer, Dept of Plant Sciences, University of Cambridge 1984-1989 Assistant Lecturer, Dept of Plant Sciences, University of Cambridge 1983-1984 Temporary Lecturer, Dept of Botany, University of Cambridge 1981-1983 Postdoctoral RA with Dr John Gray, Dept of Botany, University of Cambridge
AWARDS AND FELLOWSHIPS
2017 Fellow of the Marine Biological Association of the UK 2012 Fellow of Royal Society of Biology 2009 Erskine Fellowship, University of Canterbury, Christchurch New Zealand 2009 Best Paper Award 2008, Rebeiz Foundation for Basic Research, for Moulin et al (2008) Proc Natl Acad Sci USA 105: 15178-15183 2001 Leverhulme Study Abroad Fellowship
RELEVANT EXTERNAL COMMITTEES AND AFFILIATIONS (last 5 years)
2019-date Member, Management Board of BBSRC Network in Industrial Biotechnology & Bioenergy (NIBB) Algae-UK 2017-data Member, Steering Committee, European Algal Biomass Association (EABA) 2015-date Member & Trustee of Board of NIAB, Cambridge 2013-date Monitoring Editor, Plant Physiology 2011-2015 Member, BBSRC IBBE Strategy Advisory Panel 2011-date Member & Trustee, Council of Marine Biological Association (MBA) of the UK 2007-date Co-editor, New Phytologist
CURRENT RELEVANT GRANTS 2021-2025 Swiss National Science Foundation Sinergia: Optimizing lipid production and in-situ extraction in biofilm immobilized microalgae (CoI, with Michael Studer, UBern (PI) & Alexander Matthys, ETHZ, Switzerland and Silvia Vignolini, UCambridge) 2020-2023 HFSP: Covalent modification and regulation of proteins by CO2 using Chlamydomonas as a model system (CoI with David Vocadlo (SFU, Canada, Robert Campbell, UTokyo, Japan) 2019-2022 NSF/BBSRC: Focusing a quantitative lens on synthetic phototrophic communities (CoI with Arthur Grossman, Stanford University, CA) 2018-2021 BBSRC: (Re)design of the Chlamydomonas chloroplast (PI, with CoI Saul Purton, UCL) 2018-2021 ERANet-CoBiotech (via BBSRC): MERIT – Microalgae as renewable, innovative green cell factories (CoI, with PI Olaf Kruse, Bielefeld University, Germany and three others) 2014-to date Various impact awards for impact acceleration and/or collaboration with Industry, including BBSRC Impact Acceleration Awards, BIVs from NIBBs & Royal Society
RECENT RELEVANT PUBLICATIONS (~200 in total)
Yu Z, Geisler K, Leontidou T, Young REB, Vonlanthen SE, Purton S, Abell C, Smith AG (2021) Droplet-based microfluidic screening and sorting of microalgal populations for strain engineering applications. Algal Research, in press Shahab R, Brethauer S, Davey MP, Smith AG, Vignolini S, Luterbacher JS and Studer MH (2020) A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose. Science, 369: 6507, eabb1214 Mehrshahi P, Nguyen GTDT, Gorchs-Rovira A, Sayer A, Llavero-Pasquina M, Lim Huei Sin M, Medcalf EJ, Mendoza-Ochoa GI, Scaife MA and Smith AG (2020) Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas. ACS Synth Biol 9: 1406-1417 Gray A, Krolikowski M, Fretwell P, Convey P, Peck LS, Mendelova M, Smith AG and Davey MP (2020) Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink. Nature Commun, 11: 2527 Bunbury F, Helliwell KE, Mehrshahi P, Davey MP, Salmon DL, Holzer A, Smirnoff N and Smith AG (2020) Physiological and molecular responses of a newly evolved auxotroph of Chlamydomonas to B12 deprivation. Plant Physiol, 183:167-178 Wangpraseurt D, You S, Azam F, Jacucci G, Gaidarenko O, Hildebrand M, Kühl M, Smith AG, Davey MP, Smith A, Deheyn D, Chen S and Vignolini S (2020) Bionic 3D-printed corals. Nature Commun 11:1748 Cooper MB, Kazamia E, Helliwell KE, Kudahl UJ, Sayer A, Wheeler GL and Smith AG (2018) Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. ISME J, 13: 334–345 Peaudecerf F, Bunbury F, Bhardwaj V, Bees MA, Smith AG, Goldstein RE, Croze OA (2018) Microbial mutualism at a distance: The role of geometry in diffusive exchanges. Physical Review E 97: 022411 Crozet P, Navarro F, Willmund F, Mehrshahi P, Bakowski K, Lauersen K, Pérez-Pérez M-E, Auroy P, Gorchs Rovira A, Sauret-Gueto S, Niemeyer J, Spaniol B, Theis J, Trösch R, Westrich L-D, Vavitsas K, Baier T, Hübner W, de Carpentier F, Cassarini M, Danon A, Henri J, Marchand C, de Mia M, Sarkissian K, Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda M, Smith AG, Lemaire S (2018) Birth of a photosynthetic chassis: a MoClo toolkit enabling synthetic biology in the microalga Chlamydomonas reinhardtii. ACS Synth Biol, 7: 2074-2086 Brawley SH et al (the Porphyra Genome consortium, including Smith AG) (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA 114: E6361-E6370 Kazamia E, Helliwell KE, Purton S, Smith AG (2016) How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes. Ecol Lett, 19: 810–822 Helliwell KE, Lawrence AD, Holzer A, Kudahl UJ, Sasso S, Kräutler B, Scanlan D, Warren MJ, Smith AG (2016)
Cyanobacteria and eukaryotic algae use different chemical variants of vitamin B12. Curr Biol, 26: 999–1008 Lea-Smith DJ, Biller SJ, Davey MP, Cotton CAR, Perez Supulveda BM, Turchyn AV, Scanlan DJ, Smith AG, Chisholm SW, Howe CJ (2015) Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle PNAS 112: 13591-13596
Active Collaborator List for Alison Smith
Last Name, First Name (Affiliation) co-Author Collaborator Advisee Banadda, Nobel (Makerere University, Kampala, Uganda) X Bhaya, Devaki (Carnegie Institution of Science, CA, USA) X Campbell, Robert (University of Tokyo, Japan) X Cebon, David (University of Cambridge, UK) X Chin, Jason (MRC-Laboratory of Molecular Biology, Cambridge, UK) X Cicuta, Pietro (University of Cambridge, UK) X X Colesie, Claudia (University of Edinburgh, UK) X Convey, Peter (British Antarctic Survey, Cambridge, UK) X X Davey, Matt (Scottish Association for Marine Science, Oban, UK) X X X Fretwell, Peter (British Antarctic Survey, Cambridge, UK) X X Grossman, Arthur (Carnegie Institution of Science, CA, USA) X X Haznedaroglu, Berat (Bogazici University, Istanbul, Turkey) X Helliwell, Katherine (Marine Biological Association, UK) X X X Hippler, Michael (University of Münster, Germany) X X Howe, Chris (University of Cambridge, UK) X X Kruse, Olaf (Bielefeld University, Germany) X X Kuehn, Seppe (University of Chicago, IL, USA) X Leys, Natalie (Belgian Nuclear Research Center (SCK) Belgium) X Mathys, Alexander (ETH Zürich, Switzerland) X McCormick, Alistair (University of Edinburgh, UK) X X X Merchant, Sabeeha (UC Berkeley, USA) X X Molnar, Attila (University of Edinburgh, UK) X Peck, Lloyd (British Antarctic Survey, Cambridge, UK) X X Purton, Saul (University College London, UK) X X Robinson, Nigel (University of Durham, UK) X X Smirnoff, Nick (University of Exeter, UK) X X Spicer, Andrew (Algenuity Ltd, Stewartby, UK) X Studer, Michael (University of Bern, Switzerland) X Vaidyanathan, Raman (university of Sheffield, UK) X Vallon, Olivier (IBPC, Paris, France) X Vignolini, Silvia (University of Cambridge, UK) X X Vocadlo, David (Simon Fraser University, BC, Canada) X Warren, Martin (University of Kent, UK) X X Wijffels, Rene (Wageningen University, Netherlands) X X Yajnik, Chittaranjan (KEM Hospital, Pune, India) X
Rory J. Craig
Email: [email protected] Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, Edinburgh, UK
Professional Experience g
Institute of Evolutionary Biology, University of Edinburgh 2021 Postdoctoral Researcher (remote working from New Zealand)
Postgraduate Education g
Institute of Evolutionary Biology, University of Edinburgh 2016 - 2021 PhD, Evolutionary Biology
Lawrence Berkeley National Laboratory / Joint Genome Institute Sept. 2019 - Dec. 2019 Visiting student
Evolutionary Biology Centre, Uppsala University 2015 - 2016 Research assistant
Undergraduate Education f
University of Edinburgh 2009 - 2013 BSc (Hons) Biological Sciences (Evolutionary Biology honours) First Class (Overall Average Mark: 79)
Honours Project: Codon usage bias in Trypanosoma brucei Supervisor: Paul M. Sharp
Research Experience g
University of Edinburgh (PhD Awarding institute) University of Toronto (PhD co-supervised with visits totalling six months)
Thesis: The Evolutionary Genomics of Chlamydomonas Supervisors: Peter D. Keightley, Nick Colegrave & Rob W. Ness
My PhD research concerned the evolutionary genomics of the green alga Chlamydomonas reinhardtii and its close relatives. I used population genetics, comparative genomics and long-read sequencing approaches to address a variety of evolutionary questions and produce several important genetic and genomic resources for the species.
Lawrence Berkeley National Laboratory / Joint Genome Institute Supervisor: Sabeeha Merchant
During a three-month research visit I used PacBio RNA sequencing (i.e. Iso-Seq) to characterise widespread polycistronic gene expression in C. reinhardtii.
Uppsala University Supervisors: Hans Ellegren & Alexander Suh
I worked on avian comparative genomics, using whole-genome alignments to identify evolutionarily conserved sequences and transposable element exaptation events in avian evolution.
Publications g
Orcid: 0000-0002-6262-0008
López-Cortegano E., Craig RJ, Chebib J, Samuels T, Morgan AD, Kraemer SA, Böndel KB, Ness RW, Colegrave N & Keightley PD. (2021). De novo mutation rate variation and its determinants in Chlamydomonas. Mol Biol Evol, in press. doi:10.1093/molbev/msab140
Craig RJ, Yushenova IA, Rodriguez F & Arkhipova IR. (2021). An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes. Biorxiv https://doi.org/10.1101/2021.04.23.441226. (under review at MBE)
Chaux-Jukic F, O’Donnell S, Craig RJ, Eberhard S, Vallon O & Zhou X. (2021). Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Biorxiv https://doi.org/10.1101/2021.01.29.428817. (under review at NAR)
Gallaher DS, Craig RJ, Ganesan I, Purvine SO, McCorkle SR, Grimwood J, Strenkert D, Davidi L, Roth MS, Jeffers T, Lipton MS, Niyogi KK, Schmutz J, Theg SM, Blaby-Haas CE & Merchant SS. (2021). Widespread polycistronic gene expression in the green algal lineage. PNAS, 118, e2017714188. doi:10.1073/pnas.2017714188
Smith DR & Craig RJ (2021). Does mitochondrial DNA replication in Chlamydomonas require a reverse transcriptase? New Phytologist, 229, 1192-1195. doi:10.1111/nph.16930
Craig RJ, Hasan AR, Ness RW & Keightley PD (2021). Comparative genomics of Chlamydomonas. Plant Cell, in press. doi:10.1093/plcell/koab026
Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD & Ness RW (2019). Patters of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii. Molecular Ecology, 28(17), 3977-3993. doi:10.1111/mec.15193
Craig RJ, Suh A, Wang M & Ellegren H. (2018). Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis). Molecular Ecology, 27(2), 476-492. doi:10.1111/mec.14462
Awards and Funding g
UK Research Council / MITACS UK-Canada Globalink Doctoral Exchange Scheme (2020) Three-month research grant at the University of Toronto Value: $11,600
NERC Pilot Project grant (2018) Funding for Pacific Biosciences sequencing Value: $8,500
EASTBIO Doctoral Training Partnership PhD Programme (2016) Competitive PhD programme funded by the BBSRC Value: $22,000 (research funding) + stipend/fees
Society of Biology Top Student Award (2013) Highest undergraduate mark in the School of Biology
Community involvement g
I have acted as a reviewer for the following journals:
BMC Bioinformatics Molecular Ecology ALGAE
Tom Druet Unit of Animals Genomics GIGA-Research, ULiege Address: Unit of Animal Genomics 1, avenue de l’Hôpital – B34 (+1) B-4000 Liège tel.: 0032.43669172 e-mail: [email protected]
Education and training 1992-1993 Bachelor's degree in Mathematics (first year) University of Barcelona, Spain 1993-1998 Master’s Degree: Engineer in Agricultural Sciences - Animal Science specialization Gembloux Agricultural University – « La Plus Grande Distinction » 1998-1999 Postgraduate Advanced Diploma in Agricultural Sciences and Biological Engineering Gembloux Agricultural University – « La Plus Grande Distinction » 1998-2002 PhD in Agricultural Sciences and Biological Engineering Gembloux Agricultural University – « Félicitations du Jury »
Professional experience 1997-1998 Internship - Gembloux Agricultural University (Belgium) Early prediction of survival values of dairy cattle
1998-2002 FNRS Research fellow (PhD) - Animal Breeding Unit - Gembloux Agricultural University Additive and Non-additive Genetic Variance of Reproduction Traits in Austrian Simmental Cattle with Method R
2002-2003 FNRS Post-doctoral fellow (National Fund for Scientific Research - Belgium) Modelling of lactation curves (longitudinal data) Post-doctoral leave at SGQA - INRA (Jouy-en-Josas, France)
2003-2007 Research Engineer - Quantitative and Applied Genetics Unit - INRA (Jouy-en-Josas) Use of molecular information for genetic evaluation of dairy cattle: implementation of a Marker Assisted Selection, QTL detection and fine-mapping
2007-2009 Research Assistant - Unit of Animal Genomics (University of Liege, Belgium) Implementation of Genomic Selection in Belgian Blue cattle
2009-2017 FNRS Research Associate - Unit of Animal Genomics (University of Liege, Belgium) Statistical Genomics applied to the study and the management of livestock populations
2017-present FNRS Senior Research Associate - Unit of Animal Genomics (University of Liege, Belgium) Studying and modelling the mosaic structure of the genome in wild and domesticated populations
Selected publications
I’m currently involved in a project studying genetic architecture of quantitative traits in Chlamydomonas reinhardtii through a MAGIC design. So my selected publications focus on methods and studies to explore genetic architecture of complex traits.
Druet T, Farnir F (2011) Modeling of identity-by-descent processes along a chromosome between haplotypes and their genotyped ancestors. Genetics 188: 409-419.
Kadri NK, Sahana G, Charlier C, Iso-Touru T, Guldbrandsten B, Karim L, Nielsen US, Panitz F, Aamand GP, Schulman N, Georges M, Vilkki J, Lund MS, Druet T (2014) A 660-Kb deletion with antagonistic affects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock. PLoS Genet 10(1): e1004049.
Kadri NK, Harland C, Faux P, Cambisano N, Karim L, Coppieters W, Fritz S, Mullaart E, Baurain D, Boichard D, Spelman R, Charlier C, Georges M, Druet T (2016) Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle. Genome Res. 26(10): 1323- 1332.
Druet T, Georges M (2010) A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. Genetics 184: 789- 798.
Druet T, Gautier M (2017) A model‐based approach to characterize individual inbreeding at both global and local genomic scales. Mol. Ecol. 2620): 5820-5841.
Karim L*, Takeda H*, Lin L*, Druet T*, Arias JA, et al. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat Genet 43: 405-413.
Druet T, Macleod IM, Hayes BJ (2014) Towards genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity 112(1):39- 47.
Zhang Z, Guillaume F, Sartelet A, Charlier C, Georges M, Farnir F, Druet T (2012) Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification. Bioinformatics 28(19): 2467-2473.
Druet T, Ahariz N, Cambisano N, Tamma N, Michaux C, et al. (2014) Selection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle. BMC Genomics 15:796.
Druet T, Fritz S, Boussaha M, Ben-Jemaa S, Guillaume F, et al. (2008) Fine mapping of quantitative trait loci affecting female fertility in dairy cattle on BTA03 using a dense single-nucleotide polymorphism map. Genetics 178: 2227-2235.
Denis BAURAIN [https://orcid.org/0000-0003-2388-6185] Associate Professor of Bioinformatics University of Liège (ULiège), Belgium
Education • 1998-10 to 2003-01 | PhD in Plant Molecular Biology, ULiège • 1993-09 to 1997-10 | Masters in Plant Molecular Biology, ULiège • 1991-09 to 1994-06 | Bachelors in Software Engineering, Institut Saint-Laurent, Liège
Professional experience • 2014-10 to present | Associate Professor in Bioinformatics, ULiège • 2011-10 to 2014-09 | Assistant Professor in Bioinformatics, ULiège • 2007-10 to 2011-09 | Postdoctoral Research Assistant in Bioinformatics, ULiège • 2003-10 to 2007-09 | Postdoctoral Researcher in Molecular Phylogenetics, ULiège • 2005-10 to 2006-09 | Postdoctoral Researcher in Phylogenomics, University of Montreal (UdeM) • 2005-07 to 2005-09 | Postdoctoral Researcher in Phylogenomics, ARC Centre in Bioinformatics Genomics and Computational Biology, Brisbane, Queensland, Australia • 2003-06 to 2003-09 | Postdoctoral Researcher in Bioinformatics, ULiège • 1997-12 to 1998-05 | Research Assistant in Molecular Phylogenetics, ULiège
Institutional and external activities • 2019-04 to present | Associate Editor (section Evolutionary and Population Genetics), Frontiers Media SA, Lausanne, VD, Switzerland • 2020 to 2021 | Guest Editor (Genes), Multidisciplinary Digital Publishing Institute AG, Basel, BS, Switzerland • 2018 to 2020 | Vice-President (FRIA LS2 - Jury 1), F.R.S.-FNRS, Brussels, Belgium • 2018 | Member (Commission SEN-4 / Bourses et Mandats), F.R.S.-FNRS, Brussels, Belgium
Awards • 2003 | Prix Joseph Schepkens (Génétique végétale, triennale 2000-2002), Académie Royale de Belgique, Bruxelles, Belgium
Current relevant grants
• Granting Institution: BRAIN-be 2.0 (Pillar 2 Call 2019) Award Title: BCCM collections in the genomic era (B2/191/P2/BCCM GEN-ERA) Role and budget: Partner PI (20,000 EUR) Start: April 2020 (2 years) • Granting Institution: F.R.S-FNRS (CDR Call 2019) Award Title: Metagenomics of the rhizosphere of the metal hyperaccumulators Arabidopsis halleri and Noccaea caerulescens Role and budget: PI (60,000 EUR) Start: October 2019 (2 years) • Granting Institution: ANR (AAPG ANR 2018) Award Title: MATHTEST – Testing the Ménage à Trois Hypothesis (ANR-18-CE13-0027) Role and budget: Partner PI / Ph.D grant (~144,000 EUR) + 10,000 EUR Start: October 2018 (4 years)
- 1 - • Granting Institution: F.R.S-FNRS (FRIA Call 2018) Award Title: In silico prediction of the cell wall of microbial dark matter bacteria Role and budget: Promoter of the Ph.D candidate / Ph.D grant (~100,000 EUR) Start: October 2018 (4 years) • Granting Institution: F.R.S-FNRS (FRIA Call 2017) Award Title: Metagenomics of the rhizosphere of the metal hyperaccumulator Arabidopsis halleri Role: Co-Promoter of the Ph.D candidate / Ph.D grant (~144,000 EUR) + 10,000 EUR Start: October 2017 (4 years)
Recent relevant publications (~50 in total) 1. Van Vlierberghe M, Philippe H, Baurain D. 2021. Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages. BMC Res Notes 14. 2. Léonard RR, Leleu M, Van Vlierberghe M, Cornet L, Kerff F, Baurain D. 2021. ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies. PeerJ 9. 3. Cornet L, Magain N, Baurain D, Lutzoni F. 2021. Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: a case study with Cyanobacteria and cyanolichens. Mol Phylogenet Evol: 107100. 4. Zanatta F, Engler R, Collart F, Broennimann O, Mateo RG, Papp B, Munoz J, Baurain D, Guisan A, Vanderpoorten A. 2020. Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities. Nat Commun 11: 5601. 5. Meunier L, Tocquin P, Cornet L, Sirjacobs D, Leclere V, Pupin M, Jacques P, Baurain D. 2020. Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects. Bioinformatics 36: 4345-4347. 6. Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclere V. 2019. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 37: 107449. 7. Di Franco A, Poujol R, Baurain D, Philippe H. 2019. Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences. BMC Evol Biol 19: 21. 8. Demoulin CF, Lara YJ, Cornet L, Francois C, Baurain D, Wilmotte A, Javaux EJ. 2019. Cyanobacteria evolution: Insight from the fossil record. Free Radic Biol Med 140: 206-223. 9. Naome A, Maciejewska M, Calusinska M, Martinet L, Anderssen S, Adam D, Tenconi E, Deflandre B, Coppieters W, Karim L, Hanikenne M, Baurain D, Delfosse P, van Wezel GP, Rigali S. 2018. Complete Genome Sequence of Streptomyces lunaelactis MM109(T), Isolated from Cave Moonmilk Deposits. Genome Announc 6. 10. Maciejewska M, Calusinska M, Cornet L, Adam D, Pessi IS, Malchair S, Delfosse P, Baurain D, Barton HA, Carnol M, Rigali S. 2018. High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits. Antibiotics (Basel) 7. 11. Cornet L, Wilmotte A, Javaux EJ, Baurain D. 2018. A constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria). BMC Res Notes 11: 435. 12. Cornet L, Meunier L, Van Vlierberghe M, Leonard RR, Durieu B, Lara Y, Misztak A, Sirjacobs D, Javaux EJ, Philippe H, Wilmotte A, Baurain D. 2018. Consensus assessment of the contamination level of publicly available cyanobacterial genomes. PLoS One 13: e0200323. 13. Cornet L, Bertrand AR, Hanikenne M, Javaux EJ, Wilmotte A, Baurain D. 2018. Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures. Microb Genom 4. 14. Adam D, Maciejewska M, Naome A, Martinet L, Coppieters W, Karim L, Baurain D, Rigali S. 2018. Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria
- 2 - from Cave Moonmilk Deposits. Antibiotics (Basel) 7. 15. Simion P, Philippe H, Baurain D, Jager M, Richter DJ, Di Franco A, Roure B, Satoh N, Queinnec E, Ereskovsky A, Lapebie P, Corre E, Delsuc F, King N, Worheide G, Manuel M. 2017. A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals. Curr Biol 27: 958-967. 16. Rodriguez A, Burgon JD, Lyra M, Irisarri I, Baurain D, Blaustein L, Gocmen B, Kunzel S, Mable BK, Nolte AW, Veith M, Steinfartz S, Elmer KR, Philippe H, Vences M. 2017. Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Mol Phylogenet Evol 115: 16-26. 17. Philippe H, Vienne DMd, Ranwez V, Roure B, Baurain D, Delsuc F. 2017. Pitfalls in supermatrix phylogenomics. European Journal of Taxonomy 283: 1-25. 18. Mauroy A, Taminiau B, Nezer C, Ghurburrun E, Baurain D, Daube G, Thiry E. 2017. High- throughput sequencing analysis reveals the genetic diversity of different regions of the murine norovirus genome during in vitro replication. Arch Virol 162: 1019-1023. 19. Maciejewska M, Adam D, Naome A, Martinet L, Tenconi E, Calusinska M, Delfosse P, Hanikenne M, Baurain D, Compere P, Carnol M, Barton HA, Rigali S. 2017. Assessment of the Potential Role of Streptomyces in Cave Moonmilk Formation. Front Microbiol 8: 1181. 20. Lara Y, Durieu B, Cornet L, Verlaine O, Rippka R, Pessi IS, Misztak A, Joris B, Javaux EJ, Baurain D, Wilmotte A. 2017. Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica). Genome Announc 5. 21. Joris M, Schloesser M, Baurain D, Hanikenne M, Muller M, Motte P. 2017. Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors. Nucleic Acids Res 45: 9547-9557. 22. Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire JY, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H. 2017. Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nat Ecol Evol 1: 1370-1378. 23. Crasson O, Courtade G, Leonard RR, Aachmann FL, Legrand F, Parente R, Baurain D, Galleni M, Sorlie M, Vandevenne M. 2017. Human Chitotriosidase: Catalytic Domain or Carbohydrate Binding Module, Who's Leading HCHT's Biological Function. Sci Rep 7: 2768.
Active collaborators • Dr. Annick WILMOTTE, ULiège • Dr. Marc HANIKENNE, ULiège • Dr. Pierre CARDOL, ULiège • Prof. Emmanuelle JAVAUX, ULiège • Dr. Frédéric KERFF, ULiège • Prof. Sébastien MASSART, ULiège • Prof. Hervé VANDERSCHUREN, ULiège / KUL • Dr. Hervé PHILIPPE, Centre de Théorisation et de Modélisation de la Biodiversité, USR CNRS 2936, Moulis, France • Prof. Steven BALL, UMR 8576 CNRS/Université de Lille, France
- 3 - Dr. Marc Hanikenne Department of Life Sciences, InBioS-PhytoSystems, University of Liège, Belgium URL: https://tinyurl.com/2xc476nw Email: [email protected]
EDUCATION
2003 PhD in Sciences – University of Liège 1999 Master in Plant Biology – University of Liège 1997 BSc in Biology – University of Liège
PROFESSIONAL EXPERIENCE
2019-date Senior Research Associate (F.R.S.-FNRS), InBioS, University of Liège 2010/2019 Research Associate (F.R.S.-FNRS), InBioS, University of Liège 2006/2010 Postdoctoral Researcher (F.R.S.-FNRS), University of Liège 2003/2006 Postdoctoral Researcher, Max-Planck Institute of Plant Molecular Physiology, Potsdam, Germany 02-05 2001 Visiting PhD student, Department of Biology, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
AWARDS
2009 Joseph Schepkens Prize - Genetics (2006-2008), Belgian Royal Academy of Sciences 2001 Travel award Contest, Belgium, 2001 2000-2007 Several travel awards, Belgian Royal Academy of Sciences
INSTITUTIONAL AND EXTERNAL ACTIVITIES (last 5 years)
2021-date Associate Editor, Frontiers in Plant Science (Plan nutrition section) 2016-date Research Council, University of Liège 2015-date Co-founder and Director of Hedera-22 SA, a spin-off of ULiège
CURRENT RELEVANT GRANTS 2021-2022 FNRS: ‘Genetic architecture of zinc homeostasis in Brachypodium’ (PI) 2018-2021 FNRS: ‘Mechanisms of plant growth adaptation in extreme environments’ (PI, col with N. Verbruggen, U. Brussels) 2017-2021 ARC/ULiège: 'A MAGIC design to study photosynthesis and nutrient homeostasis in Chlamydomonas reinhardtii' (Col. With P. Cardol and T. Druet, ULiège) 2016-2022 European Fund for Regional Development, Research and Innovation program: ‘Ecosol: Attractiveness, greening and valorization of industrial wasteland during pre- and post-sanitation periods’. (Coordinator, 5 ULiège partners).
RECENT RELEVANT PUBLICATIONS (~50 in total)
Corso M, An X, Jones CY, Doblas VG, Schvartzman MS, Malkowski E, Willats WGT, Hanikenne M, & Verbruggen N (2021) Adaptation of Arabidopsis halleri to extreme metal pollution through limited metal accumulation involves changes in cell wall composition and metal homeostasis. New Phytol doi: 10.1111/nph.17173 Hanikenne M, Esteves SM, Fanara S, & Rouached H (2021). Coordinated homeostasis of essential mineral nutrients: a focus on iron. J Exp Bot doi: 10.1093/jxb/eraa483 Spielmann J, Ahmadi H, Scheepers M, Weber M, Nitsche S, Carnol M, Bosman B, Kroymann J, Motte P, Clemens S, & Hanikenne M (2020) The two copies of the zinc and cadmium ZIP6 transporter of Arabidopsis halleri have distinct effects on cadmium tolerance. Plant Cell Environ 43:2143-2157 Scheepers M, Spielmann J, Boulanger M, Carnol M, Bosman B, De Pauw E, Goormaghtigh E, Motte P, & Hanikenne M (2020) Intertwined metal homeostasis, oxidative and biotic stress responses in the Arabidopsis frd3 mutant. Plant J 102:34-52 Debode F, Hulin J, Charloteaux B, Coppieters W, Hanikenne M, Karim L, & Berben G (2019). Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies. Sci Rep. 9:15595 Legrand S, Caron T, Maumus F, Schvartzman S, Quadrana L, Durand E, Gallina S, Pauwels M, Mazoyer C, Huyghe L, Colot V, Hanikenne M, & Castric V (2019). Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes. Mob DNA 10:30 Karam, M.-J., Souleman, D., Schvartzman Echenique, M. S., Gallina, S., Spielmann, J., Poncet, C., Bouchez, O., Pauwels, M., Hanikenne, M.*, & Frérot, H.* (2019). Genetic architecture of a plant adaptive trait: QTL Mapping of intraspecific variation for tolerance to metal pollution in Arabidopsis halleri. Heredity 122 : 877-892 De Clerck, O., Kao, S.-M., Bogaert, K. A., Blomme, J., Foflonker, F., Kwantes, M., Vancaester, E., Vanderstraeten, L., Aydogdu, E., Boesger, J., Califano, G., Charrier, B., Clewes, R., Del Cortona, A., D'Hondt, S., Fernandez-Pozo, N., Gachon, C. M., Hanikenne, M., Lattermann, L., Leliaert, F., Liu, X., Maggs, C. A., Popper, Z. A., Raven, J. A., Van Bel, M., Wilhelmsson, P. K.I., Bhattacharya, D., Coates, J. C., Rensing, S. A., Van Der Straeten, D., Vardi, A., Sterck, L., Vandepoele, K., Van de Peer, Y., Wichard, T., & Bothwell, J. H. (2018). Insights into the Evolution of Multicellularity from the Sea Lettuce Genome. Curr Biol 28: 2921-33.e5 Corso, M., Schvartzman Echenique, M. S., Guzzo, F., Souard, F., Malkowski, E., Hanikenne, M., & Verbruggen, N. (2018). Contrasting cadmium resistance strategies in two metallicolous populations of Arabidopsis halleri. New Phytol 218:283-97 Schvartzman Echenique, M. S., Corso, M., Fataftha, N., Scheepers, M., Nouet, C., Bosman, B., Carnol, M., Motte, P., Verbruggen, N., & Hanikenne, M. (2018). Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri. New Phytol 218:269-82 Naomé, A., Maciejewska, M., Calusinska, M., Martinet, L., Anderssen, S., Adam, D., Tenconi, E., Deflandre, B., Coppieters, W., Karim, L., Hanikenne, M., Baurain, D., Delfosse, P., van Wezel, G., & Rigali, S. (2018). Complete Genome Sequence of Streptomyces lunaelactis MM109T, Isolated from Cave Moonmilk Deposits. Genome Announc 6(21), 00435-18. Cornet, L., Bertrand, A., Hanikenne, M., Javaux, E., Wilmotte, A., & Baurain, D. (2018). Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non- axenic cultures. Microbial Genomics doi: 10.1099/mgen.0.000212. S. Massoz, M. Hanikenne, B. Bailleul, N. Coosemans, M. Radoux, H.V. Miranda Astudillo, P. Cardol, V. Larosa, C. Remacle (2017). In vivo chlorophyll fluorescence screening allows the isolation of a Chlamydomonas mutant defective for NDUFAF3, an assembly factor involved in mitochondrial complex I assembly. Plant J., 17:2045-54 M. Joris, M.Schloesser, D. Baurain, M. Hanikenne, M. Muller, P. Motte (2017). Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors. Nucl Acid Res, 45: 9547-57
Active Collaborator List for Marc Hanikenne
Last Name, First Name (Affiliation) co-Author Collaborator Advisee Arsova, Borjana (Forschung Zentrum Jülich, Germany) x x x Clemens, Stephan (Bayreuth University, Germany) x x Frérot, Hélène (University of Lille, France) x x Isaure, Marie-Pierre (Université de Pau, France) x Krämer Ute (Ruhr University Bochum) x x Motte, Patrick (University of Liège, Belgium) x x Persson, Daniel (University of Copenhagen, Denmark) x Pauwels, Maxime (University of Lille, France) x x Rigali, Sébastien (University of Liège, Belgium) x x Spielmann, Julien (University of Toulouse, France) x x x Verbruggen, Nathalie (Free University Brussels, Belgium) x x Watt, Michelle (University of Melbourne, Australia) x x
• PERSONAL INFORMATION
Family name, First name: CARDOL, Pierre Researcher unique identifiers: orcid.org/0000-0001-9799-0546 Scopus Author ID: 7801585004
Date of birth: 13 of December, 1978 Nationality: Belgium
Present Work Address : Laboratory of genetics and physiology of microalgae Université de Liège, Belgique
E-mail : [email protected]
• CURRENT POSITIONS
2008– Senior Research Associate (since 2016) of the Belgian F.R.S.-FNRS (permanent position), Life Sciences Dept, Laboratory of genetics and physiology of microalgae, University of Liège, Belgium 2010 – Lecturer, Faculty of Science, University of Liège, Belgium
• PREVIOUS POSITIONS
2005-2008 : Junior researcher of F.R.S.-FNRS, Laboratory of Plant Biochemistry, University of Liège 2006-2007 : Visiting scientist in the laboratory of Molecular and Membrane Physiology of the chloroplast, Institut de Biologie Physico-chimique (IBPC), Paris, France (10/2006-10/2007) 2006 : Visiting scientist in the laboratory of Molecular Genetics, Instituto de Fisiología Celular, UNAM, Mexico (04-08/2006). 2004-2005 : Scientific collaborator F.R.S.-FNRS Laboratory of Genetics of microorganisms, University of Liège
• BIOBLIOGRAPHIC DATA
Source Scopus (june 2018) Total articles 57 (53 articles in peer-reviewed international journals; book chapters) H index 23 (excluding self-citations of all authors) Total citations 2026(excluding self-citations of all authors)
Source Google Scholar (January 2019) Total articles 60 (55 articles in peer-reviewed international journals; 5 book chapters) H index 29 Total citations 4797
• SELECTED PUBLICATIONS ON CHLAMYDOMONAS
1: Nawrocki WJ, Bailleul B, Cardol P, Rappaport F, Wollman FA, Joliot P. Maximal cyclic electron flow rate is independent of PGRL1 in Chlamydomonas. Biochim Biophys Acta Bioenerg. 2019 May 1;1860(5):425-432. doi: 10.1016/j.bbabio.2019.01.004. Epub 2019 Feb 1. PMID: 30711358.
2: Cardol P, Alric J, Girard-Bascou J, Franck F, Wollman FA, Finazzi G. Impaired respiration discloses the physiological significance of state transitions in Chlamydomonas. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15979-84. doi: 10.1073/pnas.0908111106. Epub 2009 Sep 1. Erratum in: Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):7150. PMID: 19805237; PMCID: PMC2747229.
3: Lapaille M, Thiry M, Perez E, González-Halphen D, Remacle C, Cardol P. Loss of mitochondrial ATP synthase subunit beta (Atp2) alters mitochondrial and chloroplastic function and morphology in Chlamydomonas. Biochim Biophys Acta. 2010 Aug;1797(8):1533-9. doi: 10.1016/j.bbabio.2010.04.013. Epub 2010 Apr 21. PMID: 20416275.
4: Massoz S, Larosa V, Plancke C, Lapaille M, Bailleul B, Pirotte D, Radoux M, Leprince P, Coosemans N, Matagne RF, Remacle C, Cardol P. Inactivation of genes coding for mitochondrial Nd7 and Nd9 complex I subunits in Chlamydomonas reinhardtii. Impact of complex I loss on respiration and energetic metabolism. Mitochondrion. 2014 Nov;19 Pt B:365-74. doi: 10.1016/j.mito.2013.11.004. Epub 2013 Dec 4. PMID: 24316185.
5: Godaux D, Bailleul B, Berne N, Cardol P. Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow in Chlamydomonas reinhardtii. Plant Physiol. 2015 Jun;168(2):648-58. doi: 10.1104/pp.15.00105. Epub 2015 Apr 30. PMID: 25931521; PMCID: PMC4453779.
6: Emonds-Alt B, Coosemans N, Gerards T, Remacle C, Cardol P. Isolation and characterization of mutants corresponding to the MENA, MENB, MENC and MENE enzymatic steps of 5'-monohydroxyphylloquinone biosynthesis in Chlamydomonas reinhardtii. Plant J. 2017 Jan;89(1):141-154. doi: 10.1111/tpj.13352. Epub 2016 Dec 5. PMID: 27612091; PMCID: PMC5299476.
7: Polukhina I, Fristedt R, Dinc E, Cardol P, Croce R. Carbon Supply and Photoacclimation Cross Talk in the Green Alga Chlamydomonas reinhardtii. Plant Physiol. 2016 Nov;172(3):1494-1505. doi: 10.1104/pp.16.01310. Epub 2016 Sep 16. PMID: 27637747; PMCID: PMC5100783.
• MAIN LAST RESARCH GRANTS
2019-2023 : Research project (PDR, F.R.S.-FNRS), GALOP, gain of loss of photosynthesis (promoter) 300 k€ 2017-2021 : GreenMagic, a MAGIC design to study photosynthesis and nutrient homeostasis in Chlamydomonas reinhardtii, funded by French Community of Belgium (ARC, co-promoter), 220 k€ (800 k€ total) 2016-2021: H2020 ERC Consolidator Grant (2016-2021). BEAL : Bioenergetics in microalgae : regulation and interaction of mitochondrial respiration, photosynthesis, and fermentative pathways. (promoter), 1,8 Mio€
• PATENTS
« Dark cell » (procédé de production d’hydrogène sans apport de lumière) déposé en Belgique sous le N° BE2016 5124 le 23 fév. 2016 et en PCT international le 17 fév. 2017 sous le N°PCT/EP2017/053651. « Photo cell » (procédé de production d’hydrogène avec apport lumineux) déposé en Belgique sous le N° BE2016 5125 le 23 fév. 2016 et en PCT international le 17 fév. 2017 sous le N°PCT/EP2017/053653. « Polypetide monomérique présentant une activité hydrogénase » en cours de dépôt sous le N° 19208856.5 - 1111. Le 13.11.2019
May 14, 2021 James Umen, PhD Member and PI
Dear Olivier,
Your draft proposal for a JGI Community Science Project on the Chlamydomonas pan- genome is very exciting. Natural variation can be a powerful tool for genetics and functional genomics, and has not been fully explored for C. reinhardtii. Many laboratories which work on Chlamydomonas, including my own, will benefit greatly from this resource. The broad comparison that you propose between laboratory strains and field isolates of C. reinhardtii will be a very effective way of discovering gene function. Your project will be of high importance for all of us in the Chlamydomonas community, working on many different aspects of its biology, and I enthusiastically support it.
Sincerely yours,
Jim Umen
975 N. Warson Rd. St. Louis, MO 63132 http://www.umenlab.org Tel 314.587.1689 Fax 314.587.1789 [email protected]
Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Wentworth Way, York YO10 5DD
www.mackinderlab.com Email: [email protected] 18th May 2021
Dear Olivier and Colleagues,
I am writing in full support of your JGI's Community Science Program Project titled ‘The Chlamydomonas pan-genome’. Your project will provide a step-change in our understanding of Chlamydomonas biology and evolution, which will not only benefit Chlamydomonas researchers but also the international algal community including ecologists, evolutionary biologists, and algal biotechnologists.
My Lab's research will greatly benefit from the generated resources and comparative analyses you and your team propose. As a lab studying photosynthetic processes in algae, with a primary focus on Chlamydomonas reinhardtii, we would be intensive users of the resources. Initial use would involve mining the genomes to look at variations in CO2 uptake and photosynthetic machinery across strains and linking this to the geographic isolation and environmental conditions. We are particularly interested in pyrenoid biology, a chloroplast located microcompartment where Rubisco is assembled to accelerate CO2 fixation. Comparing pyrenoid components across strains will be very beneficial for us to identify core conserved components and provide an expanded tool-box for ongoing plant engineering efforts to increase crop yields.
I look forward to the proposed resources becoming available and the exciting scientific discoveries it will bring in the field of Chlamydomonas evolution, photosynthesis, synthetic biology and green biotechnology.
Best wishes,
Luke Mackinder
Professor in Plant Biology Dr. Olivier VALLON UMR 7141 Institut de Biologie Physico-Chimique CNRS/Sorbonne Université 13 rue Pierre et Marie Curie 75005 Paris FRANCE
SCHOOL of BIOLOGICAL SCIENCES The University of Edinburgh Rutherford Building The King's Buildings Mayfield Road Edinburgh EH9 3BF Fax 0131 650 6556 16 May 2021 Telephone 0131 650 5316 e-mail: [email protected] website: http://mccormick.bio.ed.ac.uk/
In support of the JGI Community Science Project on the Chlamydomonas pan-genome
Dear Olivier,
It is my pleasure to write in strong support for the Chlamydomonas pan-genome project. A broad characterisation of the geographical diversity of isolates from the “Reinhardtinia” clade will be a fantastic resource to further the field’s discovery and understanding of gene function in Chlamydomonas reinhardtii, and to get a better grasp on an issue that is seldom explored enough in microbes – the genetic diversity within a species. This work will be of particular benefit to research in my lab in terms of new knowledge that could be gained regarding the Chlamydomonas CO2-concentrating mechanism. More widely, this resource will allow the Chlamydomonas community to advance critical questions in biological areas ranging from the relationship between eco-physiology and genome evolution and the mechanisms of speciation, to gene/protein diversity that could help to guide synthetic biology and biotechnology engineering efforts that will further develop green algae as bio-platforms.
I wish you all the best with this application.
Yours Sincerely,
Dr Alistair McCormick Reader in Plant Molecular Physiology & Synthetic Biology
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
May 18, 2021 Re: Support Letter – Olivier Vallon for JGI Community Science Program
Dear Olivier,
I enthusiastically support your project, the Chlamydomonas Pan Genome. I understand that the main and immediate objectives are to generate a library of Chlamydomonas variants (both established lines and new variants from nature that will be collected in the field) and to correlate genotypes and phenotypes within the set of variants. The phenotypic differences among these variants will provide new insights into numerous biological processes including photosynthesis, nutrient uptake and assimilation, carbon and nitrogen metabolism and photoprotection. Genome and transcriptome sequencing and assembly will mostly be performed by JGI (PacBio) from cells grown phototrophically, heterotrophically and myxotrophically; variation in the transcript abundances and temporal patterns of expression under the different conditions will lead to insights concerning differences in features, mechanisms and regulation of biological processes among the strains. The Co-PIs involved in this project are among the best researchers working on Chlamydomonas and the data generated will be made immediately available to the entire community for analysis.
I believe that the work generated over the course of this project and from the genome and transcriptome libraries constructed, sequenced and assembled, will be an enormously valuable resource that will be exploited by many to link genotypes to phenotypes, to develop an in-depth understanding of numerous biological processes, to work toward building a Chlamydomonas pan genome that will elucidate functional, regulatory and evolutionary processes. I have no hesitation at all in recommending that JGI partner in this exciting project, which will yield numerous short- and long-term benefits.
Sincerely yours,
Arthur Grossman
Senior Staff Scientist Carnegie Institution for Science Department of Plant Biology Stanford, CA 94305 AND Professor by Courtesy Department of Biological Sciences Stanford University Stanford, CA 94305
HUMBOLDT-UNIVERSITÄT ZU BERLIN INSTITUT FÜR BIOLOGIE, EXPERIMENTELLE BIOPHYSIK PROF. DR. DR. hc PETER HEGEMANN
HERTIE-PROFESSOR FÜR BIOPHYSIK UND NEUROWISSENSCHAFTEN
Humboldt-Universität zu Berlin • Unter den Linden 6 • 10099 Berlin
Olivier VALLON Location: Invalidenstraße 42 UMR 7141 10115 Berlin Institut de Biologie Physico-Chimique Raum 402 CNRS/Sorbonne Université Telefon 030-2093 98272 / 71 13 rue Pierre et Marie Curie https://www.biologie.hu- berlin.de/de/gruppenseiten/expbp 75005 Paris E-Mail [email protected] FRANCE Datum 17.05.2021
Dear Olivier,
As you know, we are working on the Chlamydomonas physiology and the biophysics of photoreceptors for more than three decades and for a long time our difficulty was that the gene specific genetics has not been available. Now, the technology to modify any gene of interest is available and we are able to apply it to many different so called wild type strains. However, we painfully realized that the physiology of these wild type strains is quite diverse. What remains is that we do not know the origin of these large differences, and gene deletions and modifications exhibit even more dramatic differences in physiological behavior and responses in different strains / alleles. Thus, I read with great interest your draft proposal for a JGI Community Science Project on the Chlamydomonas pan- genome. Only, the broad comparison between laboratory strains and field isolates of C. reinhardtii in conjunction with local mutagenesis will allow us to discover and fully understand gene function in depth in our model organism Chlamydomonas and relatives. In our case, we need to consider allelic differences and do mutagenesis in a variety of strains under different environmental conditions to generate a deep understanding of why nature is adapting photoreceptor details like kinetics, absorption wavelength and expression levels. To unravel the facts of structure and molecular function was the past, to understand why modifications and evolution of molecular properties occurred towards an advantage for the species will be the future. Therefore, we all need your approach and I deeply hope that you will be able to convince JGI and the funding agencies to support your endeavor.
With best regards
- P. Hegemann -
[JDR1]
Dr. Olivier Vallon IBPC, Paris FranceBPC Olin n DrJjj c e
Jean-David ROCHAIX, Ph.D. Professeur honoraire Ligne directe: +41 (0) 22 379 61 87 [email protected]
Geneva, May 20 2021
Dear Olivier,
I enthusiastically give my strongest support to your proposal for assembling a Chlamydomonas pan-genome. Such an initiatiave is particularly welcome because it will greatly expand and promote research on a number important biological processes in Chlamydomonas, including chloroplast and mitochondrial biogenesis, photosynthesis, flagellar function and assembly, phototaxis and photoreceptors, cell signaling, to name just a few. I am particularly interested in the impact of the availability of a Chlamydomonas pan-genome for the analysis of the complex mechanisms of adaptation and acclimation of the photosynthetic machinery to adverse environmental conditions such as exposure to high light, heat and salt. I am confident that the results of this project will greatly benefit ongoing research in this area, but will also boost research in other fields of biology using Chlamydomonas as model system.
With best wishes,
Jean-David Rochaix
Sciences III - 30 quai Ernest-Ansermet - CH-1211 Genève 4 Tél. +41 (0) 22 379 61 11 - Fax +41 (0) 22 379 68 68 - www.molbio.unige.ch
Department of Biology Duke University Box 90338, Durham NC 27708
Masayuki Onishi, PhD Assistant Professor Email: [email protected] sites.duke.edu/onishilab 17 May 2021 Olivier Vallon UMR7141 CNRS-Sorbonne Université Institut de Biologie Physico-Chimique Paris, France
Dear Olivier,
I was very excited to read your proposal for a JGI Community Science Project on genome sequencing of isolates of new Chlamydomonas species. In the past, I used isolates of the budding yeast Saccharomyces cerevisiae to identify naturally occurring SNPs that cause phenotypic variations in the context of synthetic lethality with type-II myosin, a gene that plays a central role in cytokinesis. Similar approach in our “green yeast” should allow us to uncover many genetic alleles important for cytokinesis that our lab is primarily interested, as well as many other biological processes we as community study. In fact, such studies should now be greatly facilitated by the transcriptomic, proteomic, and phenotypic data we have accumulated within the species of C. reinhardtii. I have no doubt that your project will be of high importance for all of us in the Chlamydomonas community working on many different aspects of its biology, as well as the Ecology and Evolution community working on Viridiplantate or evolution at large. I wish you a good luck with your proposal, and look forward to utilizing this important community resource in the future.
Sincerely yours,
Masayuki Onishi, Ph.D
Telephone: 919-660-7372 Fax: 919-660-7293 www.biology.duke.edu Matthias Schleiden Institute General Botany Prof. Dr. Maria Mittag
Universität Jena · Fakultät für Biowissenschaften · 07737 Jena Dean of Faculty of Biological Sciences
Am Planetarium 1
07743 Jena
Germany
Phone: 0 36 41 9-492 01 Phone Secr.: 0 3641 9-492 00
Fax: 0 36 41 9-492 02
E - Mail: [email protected] Jena, May 15, 2021
Dear Olivier and co-PIs!
It is my great pleasure to write this letter in enthusiastic support of your proposed project ”JGI CSP: The Chlamydomonas pan-genome”.
We are currently working on two main project areas with Chlamydomonas reinhardtii (i) photoperception and (ii) microbial interactions. Both projects will highly benefit from your comparative studies on laboratory strains and especially on Chlamydomonas field isolates within the Reinhardtinia clade along with their genome information. We expect that photoreceptor functions may diverge depending on the natural environment and that your studies will also allow to detect novel properties of photoreceptors. We are also eager to use your field isolates for studies on microbial interactions. It would be great if you could maintain some of the microbes associated with the select field strains as it would directly allow to study the natural associated bacteria and fungi and their influence on algal fitness.
I sincerely hope that you will generate funds for this highly interesting international project. It will significantly enhance research on genetically tractable green algal model systems regarding studies in their natural environment and will also support our own projects perfectly well. Please do not hesitate to contact me if I can be of any further assistance.
Kind regards,
Maria Mittag (Speaker of the Phycology Section of the German Botanical Society)
Professor Stephen M King Tel: (860) 679 3347 Molecular Biology & Biophysics Fax: (860) 679 3408 Director, Central Electron Microscopy Facility Email: [email protected]
14th May 2021
Dear Olivier
I am really excited about your proposal to JGI for a Chlamydomonas pan-genome project. My lab, in collaboration with Betty Eipper, recently uncovered a cilia-based peptidergic signaling pathway in which an amidated bioactive peptide product (derived from Cre03.g204500) is released by mating gametes associated with ciliary vesicular ectosomes. Excitingly, this product acts as a chemotactic modulator attracting gametes of minus mating type but repelling plus gametes. We have now found that the amidated product precursor is subject to very complex proteolytic processing and glycosylation during trafficking through the secretory pathway and its time on the ciliary membrane. We have also identified multiple products made from a single precursor. Indeed, although some products are present in ectosomes obtained both types of gametes, we can only detect the amidated chemotactic agent in plus gametes. In addition, we have identified several hundred other Chlamydomonas genes encoding proteins with similar characteristics of pre-propeptide precursors, including an entire family of genes closely related to Cre03.g204500, suggesting that Chlamydomonas may use peptidergic signals for numerous and diverse aspects of its biology. I am certain that your pan-genome analysis of both laboratory and wildtype strains will provide fascinating biological insights into algal-based peptidergic signaling pathways.
Yours sincerely,
______Stephen M. King Professor of Molecular Biology and Biophysics Director, Electron Microscopy Facility
An Equal Opportunity Employer
263 Farmington Avenue Farmington, Connecticut 06030-3305
Telephone: (860) 679-7682 Facsimile: (860) 679-3408 or 1239
Faculty of Biology, Medicine and Health
Dr Anil Day School of Biological Sciences Michael Smith Building Manchester M13 9PT UK
18 May 2021
Dear Olivier,
JGI Community Science Project on the Chlamydomonas pan-genome
I write in support of your timely and exciting project on establishing a pan genome of Chlamydomonas. Previous isolates, such as the strains isolated in Quebec and Minnesota, are known to be highly polymorphic. The proposed project that will include new isolates and closely related species should provide a comprehensive and long-lasting pan genome resource for the research community. The assembled pan genome will rapidly advance our understanding of the gene content and associated functions of the many pathways that are unique to the green algal lineage. The results generated will support the large community of researchers across the globe working on the different molecular and biochemical pathways operating in green algae. The results will also benefit our long term research interests on understanding the evolution and functions of repeated DNA sequences, which play an important role in chromosome and genome stability but remain poorly understood.
I wish you success with your proposal.
With best wishes,
Anil Day PhD Senior Lecturer
Prachee Avasthi, PhD
ASSOCIATE PROFESSOR, DEPARTMENT OF BIOCHEMISTRY & CELL BIOLOGY
May 14, 2021
Dear Olivier,
I was thrilled to hear of your proposed project on the Chlamydomonas pan-genome for a JGI Community Science Project. This will be an invaluable resource for my own lab, especially as we are often attempting to characterize genes of unknown function. The comparison of laboratory strains and field isolates of Chlamydomonas, combined with phenotypic data, should be very informative in this regard. Specifically, as we routinely study differences in cytoskeletal function and regulation for highly conserved genes that are more well characterized in other organisms, the genetic variation within Chlamydomonas can help us narrow down the critical genomic features that may produce unique properties within our system. This project has the potential for very high impact in our work and I know for the work of many others in the Chlamydomonas community.
Sincerely,
Prachee Avasthi Associate Professor
74 College Street HB7200 • HANOVER, NH 03755 • T 603.650.1241 • [email protected]
May 16, 2021
Dr. Olivier VALLON UMR 7141 Institut de Biologie Physico-Chimique CNRS/Sorbonne Université 13 rue Pierre et Marie Curie 75005 Paris, France
Subject: The Chlamydomonas pan-genome proposal
Dear Olivier,
I read your draft proposal for a JGI Community Science Project on the Chlamydomonas pan- genome with great interest. Like many in the Chlamydomonas community, my lab will hugely benefit from this resource. The broad comparison that you propose between laboratory strains and field isolates of C. reinhardtii will be a very effective way of discovering the function of genes in our favorite model organism. As you know, my lab currently has several active projects on studying and modeling Chlamydomonas metabolism. Discoveries of new alleles, especially when linked to phenotypic data, will shed light on the workings of many Chlamydomonas genes of yet unknown function, not to mention charting the genetic diversity within the species, which has been a constant subject of wonder for many years now. I see your project as being of high importance for all of us in the Chlamydomonas community, working on many different aspects of its biology.
Good luck with your proposal.
Sincerely,
Kourosh Salehi-Ashtiani Associate Professor of Biology Center for Genomics and Systems Biology New York University Abu Dhabi Abu Dhabi, UAE, P.O. Box 129188 [email protected]
Dr Attila Molnar Institute of Molecular Plant Sciences The University of Edinburgh Rutherford Building The King’s Buildings Max Born Crescent Edinburgh EH9 3BF Tel +44 (0)131 650 5335 Fax +44 (0)131 650 8650 [email protected]
17/05/2021
Re. JGI Community Science Project on the Chlamydomonas pan-genome
Dear Olivier,
I am delighted to write a very strong letter of support for the Chlamydomonas pan-genome project.
I have been working with Chlamydomonas reinhardtii since my first postdoc in the Baulcombe lab in 2003. The Joint Genome Institute sequenced genome and the associated Phytozome database have been instrumental in discovering microRNAs in single-celled organisms for the first time (Molnar et al., 2007, Nature), and in developing a transgene-free precision gene editing system in this model green alga (Ferenczi et al., 2017, PNAS) in my lab.
The proposed pan-genome project is ambitious and exciting. It would provide a rich source of information and create resources for understanding speciation, genome evolution, gene function and adaptation. Thus, it would benefit the Chlamydomonas community and beyond. It would also inform efforts in domesticating green algae to serve as energy crops and biotechnological platforms.
I wholeheartedly support your application.
With best wishes,
Dr Attila Molnar Group Leader, Senior Lecturer Chancellor’s Fellow http://molnar.bio.ed.ac.uk/
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336 Professor Saul Purton, PhD, BSc, FHEA Professor of Algal Biotechnology DEPARTMENT OF STRUCTURAL AND MOLECULAR BIOLOGY
London, 19th May 2021
Professor Olivier Vallon UMR7141 CNRS-Sorbonne Université Institut de Biologie Physico-Chimique Paris 75005 France
Dear Olivier,
JGI Community Science Project on the Chlamydomonas pan-genome
I am writing to give my enthusiastic support for this project, both as a long-time Chlamydomonas researcher and as Director of Algae-UK, the UK’s Network in Algal Biotechnology.
As you know, I work closely with co-applicant Prof. Alison Smith studying chloroplast gene expression and regulation, with the aim of developing the Chlamydomonas chloroplast as a Synthetic Biology platform. A pan-genome database would be extremely valuable to us for comparative studies of: 1. The organization and gene content of the chloroplast genome (=plastome) across the different isolates with a view to designing, building and transplanting into the algal cell a minimal and refactored synthetic plastome. 2. The many nuclear genes encoding trans-acting factors that regulate expression of individual chloroplast genes, and which can be exploited as systems for nuclear control of transgenes within the synthetic plastome. Your own work has shown that these factors and their binding sites seem to evolve very rapidly, so it is likely that within the genomes of the field isolates we will be able to identify systems that are sufficiently evolved to serve as orthogonal controllers of the transgenes. This will allow nuclear engineering use ‘same species’ genes (i.e. cisgenics), whilst not perturbing the native regulation of the endogenous chloroplast genes.
Wearing my Algae-UK hat, I am very aware of the growing interest in the exploitation of microalgae as light- driven cell factories for the sustainable synthesis of a wide range of bio-products, both natural compounds and recombinants. Whilst Chlamydomonas has historically been considered a model organism for fundamental research and of little commercial interest, this view has changed significantly in the last few years. Researchers and companies (e.g. Triton Algal Innovations in California) have recognized that the
University College London Gower Street London WC1E 6BT Tel: +44 (0)20 7679 2675 Fax: +44 (0)20 7679 7906 Email: [email protected] ease of cultivation, GRAS status, easily digestible cell wall, and proven health benefits make Chlamydomonas attractive as a health food or as a vegan replacement for animal protein. In addition, a number of companies in Europe and Asia are exploring the use of dried whole cells of engineered Chlamydomonas for oral delivery of vaccines and other bioactives, particularly within the aquaculture and poultry industries. But, current lab strains have yet to be domesticated and adapted for intensive industrial cultivation and high productivity, and are therefore not currently commercial viable. The future of these industries requires significant strain improvements using molecular breeding approaches. The pan-genome project will be fundamental to this, providing the molecular knowledge and resources for rational phenotypic improvements in which specific genetic traits are combined through sexual crosses.
The Chlamydomonas research community has always been one of the most open, friendly and supportive – always welcoming and encouraging new investigators and creating/sharing research resources for the common good. The pan-genome project is an essential next step in this endeavour, and will be of benefit to the whole community.
I wish you success with the application!
Best regards,
Saul Purton Professor of Algal Biotechnology, UCL and Director of Algae-UK
University College London Gower Street London WC1E 6BT Tel: +44 (0)20 7679 2675 Fax: +44 (0)20 7679 7906 Email: [email protected]
David Lea-Smith Lecturer in Microbiology School of Biological Sciences Norwich Research Park University of East Anglia Norwich NR4 7TJ UK Direct line 01223-765945 Fax 01223-333345 Email [email protected]
Norwich, 17th May, 2021
Dear Olivier,
JGI Community Science Project on the Chlamydomonas pan-genome
I am happy to support this exciting project which will significantly increase our understanding of diversity in Chlamydomonas strains from varying environments and how they differ from laboratory cultivated strains. Of particular interest to my research group will be identification of gene conserved in different isolates and how this links to essential functions conserved across the genus. Although my work predominantly focuses on cyanobacteria, I have a strong interest in characterising the function of gene products conserved across the photosynthetic lineage. An example of this is our Human Frontier Science Program funded project characterising the physiological role of hydrocarbons produced in cyanobacteria and many algae species, including Chlamydomonas reinhardtii. Therefore, I have no doubt that if funded, the results gained from this project will greatly benefit my research and the large community investigating photosynthetic microbes, and the processes and metabolic pathways conserved in these species.
Yours sincerely,
David Lea-Smith PhD