DOCSLIB.ORG

Genome Complexity in a Lean, Mean Photosynthetic Machine

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome Complexity in a Lean, Mean Photosynthetic Machine COMMENTARY Genome complexity in a lean, mean photosynthetic machine John M. Archibald* Canadian Institute for Advanced Research, Program in Evolutionary Biology, and Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, Canada B3H 1X5 hotosynthetic organisms come in et al. (1) weighs in at 12.56 Mbp, mak- all shapes and sizes. From a hu- ing it among the smallest, although not man perspective, the trees and the smallest, nuclear genome of a free- plants of dry land are the most living eukaryote characterized thus far Pconspicuous examples, but the next time [that honor belongs to the 9.2-Mbp ge- you admire a colorful tulip or marvel at nome of the fungus Ashbya gossypii the girth of a giant Sequoia, consider (14)]. The O. tauri genome is composed the following: Approximately half of the of 20 linear chromosomes between 1.07 oxygen we breathe is generated by single- and 0.16 Mbp (1) and, given its small celled photosynthesizers, phytoplankton, size, is remarkable in the number of adrift in the world’s oceans, invisible to genes it encodes: 8,166 protein-coding the naked eye and unfathomably large genes are predicted (6,265 by similarity in number, quietly harnessing solar en- to known genes), far more than in the ergy, fixing carbon dioxide, and produc- Ϸ16-Mbp genome of the red alga Cyan- ing oxygen by the bucket-load. In this idioschyzon merolae (5,331 genes) (15) issue of PNAS, Derelle et al. (1) present or in the Ϸ12-Mbp genome of the labo- the complete genome sequence of the ratory yeast Saccharomyces cerevisiae smallest of the small eukaryotic (nucle- (6,563 genes) (16). With a mean inter- us-containing) phytoplankton, Ostreo- genic distance of only 197 bp, an aver- coccus tauri. This organism is best Fig. 1. Transmission electron micrograph of O. age intron size of 103 bp, and multiple known for its diminutive cell size, about tauri strain OTH95, modified and reproduced gene fusions, the O. tauri genome ap- that of a typical bacterium. Its genome with permission from Herve´Moreau (Universite´ pears to be the product of intense ge- is equally remarkable for its small size Paris, Paris, France). C, chloroplast; S, starch gran- nome compaction. One wonders to what ule; M, mitochondrion; N, nucleus. and extreme compactness. However, the extent the complexities of transcription O. tauri genome is also unexpectedly initiation and termination have been complex and provides a fascinating refs. 6–8). O. tauri was first discovered affected. glimpse into the genetic makeup and in 1994 in France’s Thau lagoon, a shal- In terms of structure, the most un- metabolic potential of the smallest low offshoot of the Mediterranean Sea usual feature of the O. tauri genome is known eukaryote at the base of the ma- known for its oyster farming. Barely 1 its heterogeneity. The genome as a rine food chain. ␮m in diameter and practically invisible whole has a GϩC content of Ϸ58%, but Oxygenic photosynthesis first evolved under the light microscope, O. tauri was chromosome 19 and approximately half in the ancestors of modern-day cya- detected by flow cytometry and hailed of chromosome 2 differ significantly nobacteria. In terms of sheer numbers, as the ‘‘smallest eukaryotic organism’’ from this average (54% and 52% GϩC, these organisms dominate the ocean (2), (9). It also proved to be shockingly sim- respectively) and contain 77% of the but from the perspective of primary pro- ple in its ultrastructure: O. tauri cells 417 transposable elements encoded in ductivity, eukaryotic algae are consid- lack flagella and a cell wall and contain the genome (1). Genes encoded in the ered more significant. Marine diatoms, one mitochondrion, one chloroplast, a low GϩC portion of chromosome 2 also for example, produce up to 40% of the single Golgi apparatus, and a nucleus exhibit a different codon usage pattern organic carbon generated in the ocean containing a single nuclear pore (Fig. 1) than genes elsewhere in the genome, each year (3) and represent just one of (10). Molecular data (11, 12) indicate and they possess smaller and more com- the abundant and well studied algal lin- that O. tauri belongs to a group of positionally biased introns. From a phy- eages in the sea. Least understood of all green algae called prasinophytes, a lin- logenetic perspective, 43% of the genes eukaryotic phytoplankton are those with eage thought to be of key importance on chromosome 2 are most similar to a diameter of Ͻ2–3 ␮m, the so-called in elucidating the earliest events in the green algal homologs, which is a similar ‘‘picoeukaryotes.’’ The first descriptions evolution of chlorophyll b-containing proportion to that seen for the other of bacterial-sized eukaryotes date back organisms. O. tauri appears to be ubiq- chromosomes (excluding chromosome more than 40 years (e.g., ref. 4), but it is uitous in coastal waters and in the open 19). Therefore, despite its anomalous only with the application of flow cytom- ocean (e.g., refs. 6, 8, and 12), and its composition and structure, there is no etry (2) and molecular approaches (5) minimal cell structure and high growth evidence that the low GϩC region of to the study of marine microbes that we rate have made it a promising model chromosome 2 is of exogenous origin. have begun to grasp the extent of their picoeukaryote. Derelle et al. (1) raise the possibility abundance and diversity. Preliminary molecular investigations that it is a sex chromosome, citing the O. tauri is perhaps the most famous of pegged the O. tauri genome at well un- all picoeukaryotes and, together with its der 15 megabase pairs (Mbp) (11), and, close relatives, has become the focus of like most model organisms these days, Conflict of interest statement: No conflicts declared. concerted efforts to understand the O. tauri quickly became the focus of a See companion article on page 11647. global distribution and ecological signifi- genome project (13). The complete ge- *E-mail: [email protected]. cance of eukaryotic picoplankton (e.g., nome sequence presented by Derelle © 2006 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0605255103 PNAS ͉ August 1, 2006 ͉ vol. 103 ͉ no. 31 ͉ 11433–11434 Downloaded by guest on September 25, 2021 fact that bona fide sex chromosomes in present, as is a complex gene family those in Chlamydomonas (1). If C4 pho- other organisms are often similarly rid- encoding prasinophyte-specific light- tosynthesis does exist, it is not difficult dled with transposable elements (17). harvesting antenna proteins. Most to imagine the competitive advantage it Meiosis has never been observed in O. unexpected is the presence of genes would bestow on O. tauri cells under tauri, although the presence of a near- implicated in C4 photosynthesis. This conditions of high cell density and low complete set of meiotic genes encoded process has evolved repeatedly in CO2 levels. in its genome (1) suggests that sex is at higher plants as an adaptation to envi- In summary, given its small size, the least a possibility. ronmental stress (e.g., drought and low O. tauri genome packs plenty of sur- The composition of chromosome 19 is CO2 concentrations) and involves mod- prises. However, as is so often the case even more intriguing. More than 60% of ifications to leaf structure and altered in comparative genomics, the biological the predicted protein genes on this chro- biochemistry (reviewed in ref. 18). The significance of many of its interesting mosome have no similarity to known existence of bona fide C4 photosynthe- features will be fully revealed only by genes, and, of those that do, only 18% sis in phytoplankton is controversial. comparison to closely related genomes. are demonstrably green algal in origin. The morphological transformations It is therefore significant that the strain The bulk of the remaining genes appear that occur in plants are obviously im- sequenced by Derelle et al. (1) (OTH95, most similar to bacterial homologs (al- possible for a microbe, but an intracel- the original Thau Lagoon isolate) is the though modestly so), and a significant lular C4 cycle has been documented first of a trio of complete Ostreococcus fraction of the non-green algal genes are genomes soon to be available. The Joint predicted to encode surface membrane Genome Institute (www.jgi.doe.gov) has proteins and proteins involved in glyco- The most already sequenced the genome of a Cali- conjugate synthesis (1). Based on these fornian surface-isolated strain (CCE9901; observations, the authors hypothesize unusual feature of see ref. 8) and is now sequencing a ‘‘low- that chromosome 19 has a different evo- light’’ strain from the Atlantic Ocean lutionary history than the rest of the the Ostreococcus tauri (RCC141; see ref. 7). Recent work by genome (1). Given that O. tauri lacks a Moreau, Vaulot, and colleagues (7) has cell wall and is susceptible to grazing in genome is its revealed that these and other Ostreococcus nature (8), it is tempting to speculate strains constitute different ‘‘ecotypes’’ that the cell surface genes on chromo- heterogeneity. with distinct growth patterns, karyo- some 19 were acquired by lateral gene types, and pigment compositions. As transfer and selected for as an adapta- was the case for the cyanobacterium tion to predation. If this is true, how- in several plants, including the aquatic Prochlorococcus (20), a comparison of ever, how these genes were acquired, monocot Hydrilla verticillata (19). O. the genomic differences between ecolog- and from where, remains a mystery. tauri appears to possess the right com- ically distinct Ostreococcus strains should What does the O.
Load more

Recommended publications
  • Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus
    Genome analysis of the smallest free-living eukaryote SEE COMMENTARY Ostreococcus tauri unveils many unique features Evelyne Derellea,b, Conchita Ferrazb,c, Stephane Rombautsb,d, Pierre Rouze´ b,e, Alexandra Z. Wordenf, Steven Robbensd, Fre´ de´ ric Partenskyg, Sven Degroeved,h, Sophie Echeynie´ c, Richard Cookei, Yvan Saeysd, Jan Wuytsd, Kamel Jabbarij, Chris Bowlerk, Olivier Panaudi, BenoıˆtPie´ gui, Steven G. Ballk, Jean-Philippe Ralk, Franc¸ois-Yves Bougeta, Gwenael Piganeaua, Bernard De Baetsh, Andre´ Picarda,l, Michel Delsenyi, Jacques Demaillec, Yves Van de Peerd,m, and Herve´ Moreaua,m aObservatoire Oce´anologique, Laboratoire Arago, Unite´Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France; cInstitut de Ge´ne´ tique Humaine, Unite´Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France; dDepartment of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and eLaboratoire Associe´de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, 9052 Ghent, Belgium; fRosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149; gStation Biologique, Unite´Mixte de Recherche 7144, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP74, 29682 Roscoff Cedex, France; hDepartment of Applied Mathematics, Biometrics and
    [Show full text]
  • Simplified Transformation of Ostreococcus Tauri Using
    G C A T T A C G G C A T genes Technical Note Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol Frédéric Sanchez 1, Solène Geffroy 2, Manon Norest 1, Sheree Yau 1, Hervé Moreau 1 and Nigel Grimsley 1,* 1 CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France; [email protected] (F.S.); [email protected] (M.N.); [email protected] (S.Y.); [email protected] (H.M.) 2 IFREMER, Centre Atlantique, 44331 Nantes CEDEX 03, France; solene.geff[email protected] * Correspondence: [email protected] Received: 15 March 2019; Accepted: 21 May 2019; Published: 26 May 2019 Abstract: Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20–40-fold more efficient than electroporation for the transformation of O.
    [Show full text]
  • Genome Analysis and Its Significance in Four Unicellular Algae
    J Plant Res (2008) 121:3–17 DOI 10.1007/s10265-007-0133-9 INVITED ARTICLE Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana Osami Misumi Æ Yamato Yoshida Æ Keiji Nishida Æ Takayuki Fujiwara Æ Takayuki Sakajiri Æ Syunsuke Hirooka Æ Yoshiki Nishimura Æ Tsuneyoshi Kuroiwa Received: 5 October 2007 / Accepted: 30 October 2007 / Published online: 12 December 2007 Ó The Botanical Society of Japan and Springer 2007 Abstract Algae play a more important role than land In particular, examples of post-genome studies of organelle plants in the maintenance of the global environment and multiplication in C. merolae based on analyzed genome productivity. Progress in genome analyses of these organ- information are presented. isms means that we can now obtain information on algal genomes, global annotation and gene expression. The full Keywords Algae Á Genome Á Organelle Á Metabolism Á genome information for several algae has already been Photosynthetic organisms analyzed. Whole genomes of the red alga Cyanidioshyzon merolae, the green algae Ostreococcus tauri and Chla- mydomonas reinhardtii, and the diatom Thalassiosira Introduction pseudonana have been sequenced. Genome composition and the features of cells among the four algae were com- Algae are a highly diverse group of organisms that live in a pared. Each alga maintains basic genes as photosynthetic variety of environments, such as in oceans, in fresh water, eukaryotes and possesses additional gene groups to repre- in the soil, on ice, on rock, and so on. This characteristic sent their particular characteristics. This review discusses makes algae very suitable for studies concerning the and introduces the latest research that makes the best use of adaptation of organisms to different environments, and it the particular features of each organism and the signifi- provides the possibility of finding novel genes related to cance of genome analysis to study biological phenomena.
    [Show full text]
  • Cross-Exchange of B-Vitamins Underpins a Mutualistic Interaction Between Ostreococcus Tauri and Dinoroseobacter Shibae
    The ISME Journal (2019) 13:334–345 https://doi.org/10.1038/s41396-018-0274-y ARTICLE Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae 1,3 1,4 1,5 1 1 Matthew B. Cooper ● Elena Kazamia ● Katherine E. Helliwell ● Ulrich Johan Kudahl ● Andrew Sayer ● 2 1 Glen L. Wheeler ● Alison G. Smith Received: 23 April 2018 / Revised: 30 June 2018 / Accepted: 27 July 2018 / Published online: 18 September 2018 © International Society for Microbial Ecology 2018 Abstract Ostreococcus tauri, a picoeukaryotic alga that contributes significantly to primary production in oligotrophic waters, has a highly streamlined genome, lacking the genetic capacity to grow without the vitamins thiamine (B1) and cobalamin (B12). Here we demonstrate that the B12 and B1 auxotrophy of O. tauri can be alleviated by co-culturing with a heterotrophic bacterial partner Dinoroseobacter shibae, a member of the Rhodobacteraceae family of alpha-proteobacteria, genera of which are frequently found associated with marine algae. D. shibae lacks the complete pathway to synthesise three other B- vitamins: niacin (B3), biotin (B7), and p-aminobenzoic acid (a precursor for folate, B9), and the alga is in turn able to satisfy 1234567890();,: 1234567890();,: the reciprocal vitamin requirements of its bacterial partner in a stable long-term co-culture. Bioinformatics searches of 197 representative marine bacteria with sequenced genomes identified just nine species that had a similar combination of traits (ability to make vitamin B12, but missing one or more genes for niacin and biotin biosynthesis enzymes), all of which were from the Rhodobacteraceae. Further analysis of 70 species from this family revealed the majority encoded the B12 pathway, but only half were able to make niacin, and fewer than 13% biotin.
    [Show full text]
  • Ecotype Diversity in the Marine Picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae)
    Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology 1462-2912Blackwell Publishing Ltd, 200476853859Original ArticleEcotype diversity in the picoeukaryote OstreococusF. Rodríguez et al. Environmental Microbiology (2005) 7(6), 853–859 doi:10.1111/j.1462-2920.2005.00758.x Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae) Francisco Rodríguez,1 Evelyne Derelle,2 significant role in biogeochemical processes, primary Laure Guillou,1 Florence Le Gall,1 Daniel Vaulot1 and productivity and food webs especially in oligotrophic Hervé Moreau2* areas, where it accounts typically for up to 80% of the 1Station Biologique, UMR 7127 CNRS/INSU/UPMC, BP autotrophic biomass (Campbell et al., 1994; Li, 1994; 74, 29682 Roscoff, France. Rocap et al., 2002). Over the past two decades, a large 2Laboratoire Arago, UMR 7628 CNRS/UPMC, BP44, body of knowledge has accumulated on the diversity and 66651, Banyuls-sur-mer, France. ecophysiology of the cyanobacterium Prochlorococcus (Partensky et al., 1999; Rocap et al., 2003). In particular, part of its global success has been attributed to the exist- Summary ence of distinct low- and high-light ecotypes, occupying The importance of the cyanobacteria Prochlorococ- different niches and exploiting different resources (Rocap cus and Synechococcus in marine ecosystems in et al., 2003). terms of abundance and primary production can be Picoeukaryotic cells have been initially detected by their partially explained by ecotypic differentiation. Despite characteristic flow cytometry and pigment signatures over the dominance of eukaryotes within photosynthetic large geographical and vertical scales (Andersen et al., picoplankton in many areas a similar differentiation 1996). However, the genetic and physiological traits that has never been evidenced for these organisms.
    [Show full text]
  • Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus
    Genome analysis of the smallest free-living eukaryote SEE COMMENTARY Ostreococcus tauri unveils many unique features Evelyne Derellea,b, Conchita Ferrazb,c, Stephane Rombautsb,d, Pierre Rouze´ b,e, Alexandra Z. Wordenf, Steven Robbensd, Fre´ de´ ric Partenskyg, Sven Degroeved,h, Sophie Echeynie´ c, Richard Cookei, Yvan Saeysd, Jan Wuytsd, Kamel Jabbarij, Chris Bowlerk, Olivier Panaudi, BenoıˆtPie´ gui, Steven G. Ballk, Jean-Philippe Ralk, Franc¸ois-Yves Bougeta, Gwenael Piganeaua, Bernard De Baetsh, Andre´ Picarda,l, Michel Delsenyi, Jacques Demaillec, Yves Van de Peerd,m, and Herve´ Moreaua,m aObservatoire Oce´anologique, Laboratoire Arago, Unite´Mixte de Recherche 7628, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP44, 66651 Banyuls sur Mer Cedex, France; cInstitut de Ge´ne´ tique Humaine, Unite´Propre de Recherche 1142, Centre National de la Recherche Scientifique, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France; dDepartment of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology and eLaboratoire Associe´de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, 9052 Ghent, Belgium; fRosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149; gStation Biologique, Unite´Mixte de Recherche 7144, Centre National de la Recherche Scientifique–Universite´Pierre et Marie Curie-Paris 6, BP74, 29682 Roscoff Cedex, France; hDepartment of Applied Mathematics, Biometrics and
    [Show full text]
  • Ostreococcus Tauri Is a New Model
    Lelandais et al. BMC Genomics (2016) 17:319 DOI 10.1186/s12864-016-2666-6 RESEARCHARTICLE Open Access Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton Gaëlle Lelandais1†, Ivo Scheiber2†, Javier Paz-Yepes3, Jean-Claude Lozano4, Hugo Botebol4, Jana Pilátová2, Vojtěch Žárský2, Thibaut Léger1, Pierre-Louis Blaiseau4, Chris Bowler3, François-Yves Bouget4, Jean-Michel Camadro1, Robert Sutak2* and Emmanuel Lesuisse1* Abstract Background: Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcus tauri is a very good model for studying physiological and genetic aspects of the adaptation of the green algal lineage to the marine environment: it has a very compact genome, is easy to culture in laboratory conditions, and can be genetically manipulated by efficient homologous recombination. In this study, we aimed at characterizing the mechanisms of iron assimilation in O. tauri by combining genetics and physiological tools. Specifically, we wanted to identify and functionally characterize groups of genes displaying tightly orchestrated temporal expression patterns following the exposure of cells to iron deprivation and day/night cycles, and to highlight unique features of iron metabolism in O. tauri, as compared to the freshwater model alga Chalamydomonas reinhardtii. Results: We used RNA sequencing to investigated the transcriptional responses to iron limitation in O. tauri and found that most of the genes involved in iron uptake and metabolism in O. tauri are regulated by day/night cycles, regardless of iron status. O. tauri lacks the classical components of a reductive iron uptake system, and has no obvious iron regulon.
    [Show full text]
  • An Original Adaptation of Photosynthesis in the Marine Green Alga Ostreococcus
    An original adaptation of photosynthesis in the marine green alga Ostreococcus Pierre Cardol*†‡, Benjamin Bailleul*†, Fabrice Rappaport*†, Evelyne Derelle†§, Daniel Be´ al*†,Ce´ cile Breyton¶, Shaun Baileyʈ, Francis Andre´ Wollman*†, Arthur Grossmanʈ, Herve´ Moreau†§, and Giovanni Finazzi*†** *Unite´ Mixte de Recherche 7141 and ¶Unite´ Mixte de Recherche 7099, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Universite´ Paris 7, 75005 Paris, France; †Universite´ Pierre et Marie Curie, Universite´ Paris 6, 75005 Paris, France; ‡Laboratoire de Photobiologie, De´ partement des Sciences la Vie, Universite´ de Lie` ge, B-4000 Lie` ge, Belgium; §Centre National de la Recherche Scientifique, Unite´ Mixte de Recherche 7628, MBCE, Observatoire Oce´ anologique, F-66651 Banyuls sur Mer, France; and ʈThe Carnegie Institution, Department of Plant Biology, Stanford University, Stanford, CA 94305 Communicated by Pierre A. Joliot, Institut de Biologie Physico-Chimique, Paris, France, March 20, 2008 (received for review December 15, 2007) Adaptation of photosynthesis in marine environment has been strains (12). Although the low- and high-light Ostreococcus examined in two strains of the green, picoeukaryote Ostreococcus: strains exhibit differences in their growth characteristics under OTH95, a surface/high-light strain, and RCC809, a deep-sea/low- various light regimes, it is not clear whether these differences light strain. Differences between the two strains include changes reflect long-term adaptations (speciation) or transient acclima- in the light-harvesting capacity, which is lower in OTH95, and in the tion processes. Furthermore, there is little information concern- photoprotection capacity, which is enhanced in OTH95. Further- ing the photosynthetic properties of Ostreococcus; these prop- more, RCC809 has a reduced maximum rate of O2 evolution, which erties would strongly influence growth characteristics and the is limited by its decreased photosystem I (PSI) level, a possible ecologic niche in which these organisms could thrive.
    [Show full text]
  • The Tiny Eukaryote Ostreococcus Provides Genomic Insights Into the Paradox of Plankton Speciation
    The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation Brian Palenika,b, Jane Grimwoodc, Andrea Aertsd, Pierre Rouze´ e, Asaf Salamovd, Nicholas Putnamd, Chris Duponta, Richard Jorgensenf, Evelyne Derelleg, Stephane Rombautsh, Kemin Zhoud, Robert Otillard, Sabeeha S. Merchanti, Sheila Podellj, Terry Gaasterlandj, Carolyn Napolif, Karla Gendlerf, Andrea Manuellk, Vera Taia, Olivier Vallonl, Gwenael Piganeaug,Se´ verine Jancekg, Marc Heijdem, Kamel Jabbarim, Chris Bowlerm, Martin Lohrn, Steven Robbensh, Gregory Wernerd, Inna Dubchakd, Gregory J. Pazouro, Qinghu Renp, Ian Paulsenp, Chuck Delwicheq, Jeremy Schmutzc, Daniel Rokhsard, Yves Van de Peerh, Herve´ Moreaug, and Igor V. Grigorievb,d aScripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202; cJoint Genome Institute and Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94304; dU.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598; eLaboratoire Associe´de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; fDepartment of Plant Sciences, University of Arizona, 303 Forbes Building, Tucson, AZ 85721-0036; gObservatoire Oce´anologique, Laboratoire Arago, Centre National de la Recherche Scientifique/Universite´Pierre et Marie Curie Paris 6, Unite´Mixte de Recherche 7628, BP 44, 66651 Banyuls sur Mer Cedex, France; hDepartment of Plant Systems
    [Show full text]
  • Optimizing Bioreactor Growth of the Smallest Eukaryote
    bioRxiv preprint doi: https://doi.org/10.1101/291211; this version posted March 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Optimizing bioreactor growth of the smallest eukaryote Authors: Chuck R. Smallwood1, Eric A. Hill1, William Chrisler1, Jory Brookreson1, & James E. Evans1* Affiliations: 1) Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99354, USA *Corresponding Author: [email protected] Abstract: Photosynthetic organisms are adept at circumventing nutrient deprivation. Microalgae in particular present novel adaptations to nutrient and light starvation since they can scavenge external and internal nutrient pools to redistribute energy resources for survival. In this report, a turbidostatic photobioreactor was used to characterize environmental conditions and nutrient requirements for cultures of the smallest free- living eukaryote Ostreococcus tauri. Optimized growth conditions were identified that enable 4-times faster phototrophic growth-rates while increasing total biomass 10-fold. By achieving phototrophic doubling times shorter than 6 hours, these results highlight the potential of this smallest eukaryote for future industrial bioproduct applications. 1 bioRxiv preprint doi: https://doi.org/10.1101/291211; this version posted March 28, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Introduction Ostreococcus tauri was originally isolated from copper contaminated water and it can grow in a variety of media conditions including artificial salt water (ASW) brackish media1,2 or with additives such as glycerol3.
    [Show full text]
  • Ostreococcus Tauri: Seeing Through the Genes to the Genome
    Update TRENDS in Genetics Vol.23 No.4 Research Focus Ostreococcus tauri: seeing through the genes to the genome Patrick J. Keeling Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada The marine green alga Ostreococcus tauri is the compared with other green algae and plants. There are also smallest-known free-living eukaryote. The recent sequen- several interesting features relating to the light-harvest- cing of its genome extends this distinction, because it ing antennae, the carbon assimilation machinery and the also has one of the smallest and most compact nuclear possibility of C4 photosynthesis. Overall, however, the genomes. For other highly compacted genomes (e.g. major metabolic and information-processing pathways those of microsporidian parasites and relic endosymbiont are fully represented, as expected for a free-living cell. nucleomorphs), compaction is associated with severe The O. tauri genome is not a homogeneous entity, and gene loss. By contrast, O. tauri has retained a large comp- this feature is particularly exemplified by two regions: lement of genes. Studying O. tauri should shed light on chromosome 19 and part of chromosome 2. Both of these forces, other than parasitism and endosymbiosis, that regions contain fewer genes, encode a greater density of result in densely packed genomes. transposons and have a lower G+C content than the rest of the genome. Genome heterogeneity has been observed in other organisms, including those with small and com- Genome compaction pacted genomes, but it is exceptional in O. tauri because Similar to the old adage about woods, sometimes it can be it is clearly associated with two discrete regions that differ difficult to see the genome for the genes.
    [Show full text]
  • 3-D Ultrastructure of O. Tauri: Electron
    III-1 3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell Gregory P. Henderson, Lu Gan, and Grant J. Jensen* Division of Biology, California Institute of Technology, Pasadena, CA Running Title: 3-D Ultrastructure of Ostreococcus tauri * Corresponding Author. Mail address: Caltech Division of Biology, 1200 E. California Blvd., Pasadena, CA 91125. Phone: (626) 395-5730. Fax: (626) 395-5730. E-mail: [email protected]. III-2 Abstract The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) were consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes. Abbreviations 3-D, three-dimensional; ECT, electron cryotomography; ER, endoplasmic reticulum; NE, nuclear envelope; NPC, nuclear pore complex.
    [Show full text]