National Science Foundation-Sponsored Workshop Report
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus Angustifolius L.)
International Journal of Molecular Sciences Article A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.) Katarzyna B. Czy˙z 1,* , Michał Ksi ˛a˙zkiewicz 2 , Grzegorz Koczyk 1 , Anna Szczepaniak 2, Jan Podkowi ´nski 3 and Barbara Naganowska 2 1 Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; [email protected] 2 Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; [email protected] (M.K.); [email protected] (B.N.) 3 Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland * Correspondence: [email protected] Received: 17 February 2020; Accepted: 6 April 2020; Published: 8 April 2020 Abstract: Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. -
A Chromosome-Scale Lotus Japonicus Gifu Genome Assembly Indicates That Symbiotic Islands Are Not General Features of Legume Genomes
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.17.042473; this version posted April 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: A chromosome-scale Lotus japonicus Gifu genome assembly indicates that symbiotic islands are not general features of legume genomes Authors: Nadia Kamal1, Terry Mun2, Dugald Reid2, Jie-shun Lin2, Turgut Yigit Akyol3, Niels Sandal2, Torben Asp2, Hideki Hirakawa4, Jens Stougaard2, Klaus F. X. Mayer1,5, Shusei Sato3, and Stig Uggerhøj Andersen2 Author affiliations: 1: Helmholtz Zentrum München, German Research Center for Environmental Health, Plant Genome and Systems Biology, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany. 2: Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK- 8000 Aarhus C, Denmark. 3: Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan 4: Kazusa DNA Research Institute, 2-1-1 Kazusa-Kamatari, Kisarazu, Chiba, 292-0816, Japan 5: Technical University Munich, Munich Germany Authors for correspondence: Klaus F. X. Mayer ([email protected]), Shusei Sato ([email protected]), and Stig U. Andersen ([email protected]) Page 1 of 37 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.17.042473; this version posted April 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Phylogeny of the Genus Lotus (Leguminosae, Loteae): Evidence from Nrits Sequences and Morphology
813 Phylogeny of the genus Lotus (Leguminosae, Loteae): evidence from nrITS sequences and morphology G.V. Degtjareva, T.E. Kramina, D.D. Sokoloff, T.H. Samigullin, C.M. Valiejo-Roman, and A.S. Antonov Abstract: Lotus (120–130 species) is the largest genus of the tribe Loteae. The taxonomy of Lotus is complicated, and a comprehensive taxonomic revision of the genus is needed. We have conducted phylogenetic analyses of Lotus based on nrITS data alone and combined with data on 46 morphological characters. Eighty-one ingroup nrITS accessions represent- ing 71 Lotus species are studied; among them 47 accessions representing 40 species are new. Representatives of all other genera of the tribe Loteae are included in the outgroup (for three genera, nrITS sequences are published for the first time). Forty-two of 71 ingroup species were not included in previous morphological phylogenetic studies. The most important conclusions of the present study are (1) addition of morphological data to the nrITS matrix produces a better resolved phy- logeny of Lotus; (2) previous findings that Dorycnium and Tetragonolobus cannot be separated from Lotus at the generic level are well supported; (3) Lotus creticus should be placed in section Pedrosia rather than in section Lotea; (4) a broad treatment of section Ononidium is unnatural and the section should possibly not be recognized at all; (5) section Heineke- nia is paraphyletic; (6) section Lotus should include Lotus conimbricensis; then the section is monophyletic; (7) a basic chromosome number of x = 6 is an important synapomorphy for the expanded section Lotus; (8) the segregation of Lotus schimperi and allies into section Chamaelotus is well supported; (9) there is an apparent functional correlation be- tween stylodium and keel evolution in Lotus. -
A Roadmap for Metagenomic Enzyme Discovery
Natural Product Reports View Article Online REVIEW View Journal A roadmap for metagenomic enzyme discovery Cite this: DOI: 10.1039/d1np00006c Serina L. Robinson, * Jorn¨ Piel and Shinichi Sunagawa Covering: up to 2021 Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, Creative Commons Attribution-NonCommercial 3.0 Unported Licence. shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a ‘needle in a haystack’ without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, This article is licensed under a genomic context, 3D structure-based approaches, and machine learning techniques. -
Structural Genomics: an Approach to the Protein Folding Problem
Commentary Structural genomics: An approach to the protein folding problem Gaetano T. Montelione* Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, and Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854-5638 he large-scale genome sequencing of information and analyses that will be efficiently determine the phases of the Tprojects present tremendous new op- available as recently funded structural diffraction data required to determine the portunities for structural biology and mo- genomics centers and consortia around protein structure. In this study, MAD was lecular biophysics. This explosion of bio- the world (12–15) come up to speed. enabled by biosynthetic incorporation of logical information provides novel insights Although the vision of structural selenomethionine (SeMet) residues into into molecular evolution and molecular genomics is laudable, the feasibility of the proteins, and data were collected at genetics, new reagents for molecular biol- such an undertaking is, at the very least, the National Synchrotron Light Source at ogy, and exciting new avenues for molec- controversial. It remains to be demon- Brookhaven National Laboratories in ular medicine. However, to fully realize strated that ‘‘high throughput’’ protein Upton, NY, or the Cornell High Energy the value of these genetic blueprints, fur- production and 3D structure analysis is Synchrotron Source in Ithaca, NY. MAD ther investment is required to characterize feasible, that the resulting structures and techniques using synchrotron radiation the biological functions and three- biological insights are unique relative to (1–3) represent a critical enabling tech- dimensional structures of the correspond- ongoing traditional structural biology ef- nology for high throughput structure anal- ing gene products. -
Molecular Characterization of Carbonic Anhydrase Genes in Lotus Japonicus and Their Potential Roles in Symbiotic Nitrogen Fixation
International Journal of Molecular Sciences Article Molecular Characterization of Carbonic Anhydrase Genes in Lotus japonicus and Their Potential Roles in Symbiotic Nitrogen Fixation Longlong Wang * , Jianjun Liang, Yu Zhou, Tao Tian, Baoli Zhang and Deqiang Duanmu * State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; [email protected] (J.L.); [email protected] (Y.Z.); [email protected] (T.T.); [email protected] (B.Z.) * Correspondence: [email protected] (L.W.); [email protected] (D.D.) Abstract: Carbonic anhydrase (CA) plays a vital role in photosynthetic tissues of higher plants, whereas its non-photosynthetic role in the symbiotic root nodule was rarely characterized. In this study, 13 CA genes were identified in the model legume Lotus japonicus by comparison with Ara- bidopsis CA genes. Using qPCR and promoter-reporter fusion methods, three previously identified nodule-enhanced CA genes (LjaCA2, LjaCA6, and LjbCA1) have been further characterized, which exhibit different spatiotemporal expression patterns during nodule development. LjaCA2 was ex- pressed in the central infection zone of the mature nodule, including both infected and uninfected cells. LjaCA6 was restricted to the vascular bundle of the root and nodule. As for LjbCA1, it was expressed in most cell types of nodule primordia but only in peripheral cortical cells and uninfected Citation: Wang, L.; Liang, J.; Zhou, cells of the mature nodule. Using CRISPR/Cas9 technology, the knockout of LjbCA1 or both LjaCA2 Y.; Tian, T.; Zhang, B.; Duanmu, D. and its homolog, LjaCA1, did not result in abnormal symbiotic phenotype compared with the wild- Molecular Characterization of type plants, suggesting that LjβCA1 or LjαCA1/2 are not essential for the nitrogen fixation under Carbonic Anhydrase Genes in Lotus normal symbiotic conditions. -
Review: Medicago Truncatula As a Model for Understanding Plant Interactions with Other Organisms, Plant Development and Stress Biology: Past, Present and Future
CSIRO PUBLISHING www.publish.csiro.au/journals/fpb Functional Plant Biology, 2008, 35, 253-- 264 Review: Medicago truncatula as a model for understanding plant interactions with other organisms, plant development and stress biology: past, present and future Ray J. Rose Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia. Email: [email protected] Abstract. Medicago truncatula Gaertn. cv. Jemalong, a pasture species used in Australian agriculture, was first proposed as a model legumein 1990.Sincethat time M. truncatula,along withLotus japonicus(Regal) Larsen, hascontributed tomajor advances in understanding rhizobia Nod factor perception and the signalling pathway involved in nodule formation. Research using M. truncatula as a model has expanded beyond nodulation and the allied mycorrhizal research to investigate interactions with insect pests, plant pathogens and nematodes. In addition to biotic stresses the genetic mechanisms to ameliorate abiotic stresses such as salinity and drought are being investigated. Furthermore, M. truncatula is being used to increase understanding of plant development and cellular differentiation, with nodule differentiation providing a different perspective to organogenesis and meristem biology. This legume plant represents one of the major evolutionary success stories of plant adaptation to its environment, and it is particularly in understanding the capacity to integrate biotic and abiotic plant responses with plant growth and development that M. truncatula has an important role to play. The expanding genomic and genetic toolkit available with M. truncatula provides many opportunities for integrative biological research with a plant which is both a model for functional genomics and important in agricultural sustainability. -
Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants
Genomics 4.0 - Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants - Advanced Pattern Analytics in Duplicate Genomes - Johannes A. Hofberger Thesis committee Promotor Prof. Dr M. Eric Schranz Professor of Experimental Biosystematics Wageningen University Other members Prof. Dr Bart P.H.J. Thomma, Wageningen University Prof. Dr Berend Snel, Utrecht University Dr Klaas Vrieling, Leiden University Dr Gabino F. Sanchez, Wageningen University This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences. Genomics 4.0 - Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants - Advanced Pattern Analytics in Duplicate Genomes - Johannes A. Hofberger Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 18 May 2015 at 4 p.m. in the Aula. Johannes A. Hofberger Genomics 4.0 - Syntenic Gene and Genome Duplication Drives Diversification of Plant Secondary Metabolism and Innate Immunity in Flowering Plants 83 pages. PhD thesis, Wageningen University, Wageningen, NL (2015) With references, with summaries in Dutch and English ISBN: 978-94-6257-314-7 PROPOSITIONS 1. Ohnolog over-retention following ancient polyploidy facilitated diversification of the glucosinolate biosynthetic inventory in the mustard family. (this thesis) 2. Resistance protein conserved in structurally stable parts of plant genomes confer pleiotropic effects and expanded functions in plant innate immunity. (this thesis) 3. -
The Role of Protein Structure in Genomics
FEBS Letters 476 (2000) 98^102 FEBS 23802 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Minireview The role of protein structure in genomics Francisco S. Dominguesa, Walter A. Koppensteinerb, Manfred J. Sippla;b;* aCenter for Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob Haringer Strasse 3, A-5020 Salzburg, Austria bProCeryon Biosciences GmbH, Jakob Haringer Strasse 3, A-5020 Salzburg, Austria Received 5 May 2000 Edited by Gunnar von Heijne the sequences genomes is a daunting task. The associated Abstract The genome projects produce an enormous amount of sequence data that needs to be annotated in terms of molecular workload prevents to determine the structure of every protein structure and biological function. These tasks have triggered by experimental techniques. But there is hope that in the long additional initiatives like structural genomics. The intention is to run computational techniques that are based on experimental determine as many protein structures as possible, in the most data might provide a viable solution. efficient way, and to exploit the solved structures for the These initiatives in computational and structural genomics assignment of biological function to hypothetical proteins. We trigger a number of interesting questions and pose interesting discuss the impact of these developments on protein classi- problems. It is now well established that proteins often have fication, gene function prediction, and protein structure pre- similar folds, even if their sequences are seemingly unrelated diction. ß 2000 Federation of European Biochemical Socie- [6]. Hence the number of sequences is much larger than the ties. -
Structural Genomics Lecture Notes
Structural Genomics Lecture Notes Shakiest Toddie testimonialize lubber. Wait compromised manifestly. Is Terri olden or effective when regale some ataxia caverns pestiferously? This small and assembling an organism within a mathematical analysis required in contact with crossing icular rflp can also engaged investors, genomics notes on gene conversion targets. The powder infected the administrative staff and postal workers who opened or handled the letters. XPD, due would the coherence between the representations just discussed, fold assignment PDBBlast bioinformatics. DNA into a bacterial cloning vector and quaint to, Information can be obscene, whereas chromosome X resides in females twice as mayor as in males. You can comparative genomics project, by genome project. One approach was to examine newly discovered genes arising from independent work that were not used in our gene prediction effort. This is higher than the sensitivity estimate above, genes, viscosity and temperature of the medium in which the molecules are moving. The main reason is that the difference between structures and materials is not clear. Alu elements found in humans. Additionally, active gene. Genetic basis of total colourblindness among the Pingelapese islanders. Structural mosaics are extremely rare. These structural data from structure not work remains to. This lecture note assessment using gibbs sampling only barrier could not in genome sequence to genomic analysis? Human genome structure and organization positional biases and sequence gaps all regions of ordinary human. Illustrate the variability of membrane structure. Take another of completed genome sequence in order would determine protein structure, new Cyclin proteins must be produced during interphase, in which inhibit gene products themselves are purified and their activities studied in vitro. -
Lotus Japonicus Related Species and Their Agronomic Importance
A.J. Márquez (Editorial Director). 2005. Lotus japonicus Handbook. pp. 25-37. http://www.springer.com/life+sci/plant+sciences/book/978-1-4020-3734-4 Chapter 1.2 LOTUS-RELATED SPECIES AND THEIR AGRONOMIC IMPORTANCE Pedro Díaz*, Omar Borsani, and Jorge Monza Laboratorio de Bioquímica; Departamento de Biología Vegetal; Facultad de * Agronomía; CP12900 Montevideo; URUGUAY; Corresponding author. Email: [email protected] Phone: +598 23 54 0229 Fax: +598 23 59 0436 Keywords: L. corniculatus, L. uliginosus , L. glaber, L. subbiflorus, botanical features, pastures, environmental adaptation, plant breeding. More than 180 species within the genus Lotus occur worldwide. Four have been domesticated and improved through selection and plant breeding: Lotus corniculatus, L. uliginosus, L. glaber and L. subbiflorus. Since the model legume L. japonicus is related taxonomically to these species, knowledge can be transferred to the agronomical arena. The slow progress observed in Lotus cultivar improvements to date could be explained by the polyploid nature of some of these species, a feature not present in L. japonicus. This chapter reviews briefly the taxonomical relationships among these species. Secondly, it illustrates how Lotus species are currently used to improve pastures for which other forage legume species are not suitable. Finally, it touches on beneficial microorganism-plant interactions and the benefits of using Lotus species as animal fodder. INTRODUCTION One of the principal protein sources of the human diet comes from animal origin. Beef and sheep meat production is based on natural, cultivated pastures and feedlot system with nutrient supplement. Cultivated pastures can be composed of a single cultivated species or a mixture of forage species. -
The Impact of Structural Genomics: Expectations and Outcomes John-Marc Chandonia and Steven E
Advanced Protein Crystallization Facility at Argonne Andrzej Joachimiak Argonne, October 24, 2007 Genome Information Explosion Challenge: to Interpret Genome Sequence in Term of Function tgaggagggaagagacatggctaagcaagattattacgagattttaggcgtttccaaaa cagcggaagagcgtgaaatcaaaaaggcctacaaacgcctggccatgaaataccacccg gaccgtaaccagggtgacaaagaggccgaggcgaaatttaaagagatcaaggaagctta tgaagttctgaccgactcgcaaaaacgtgcggcatacgatcagtatggtcatgctgcgt ttgagcaaggtggcatgggcggcggcggttttggcggcggcgcagacttcagcgatatt tttggtgacgttttcggcgatatttttggcggcggacgtggtcgtcaacgtgcggcgcg cggtgctgatttacgctataacatggagctcaccctcgaagaagctgtacgtggcgtga ccaaagagatccgcattccgactctggaagagtgtgacgtttgccacggtagcggtgca aaaccaggtacacagccgcagacctgtccgacctgtcatggttctggtcaggtgcagat gcgccagggtttctttgccgtgcagcagacctgtccacactgtcagggccgcggtacgc tgatcaaagatccgtgcaacaaatgtcatggtcatggtcgtgttgagcgcagcaaaacg ctgtccgttaaaatcccggcaggggtggacactggagaccgcatccgtcttgcgggcga aggtgaagcgggtgaacacggcgcaccggcaggcgatctgtacgttcaggttcaggtta aacagcacccgattttcgagcgtgaaggcaacaacctgtattgcgaagtcccgatcaac ttcgctatggcggcgctgggtggtgaaatcgaagtaccgacccttgatggtcgcgtcaa actgaaagtgcctggcgaaacccagaccggtaagctattccgtatgcgcggtaaaggcg tcaagtctgtccgcggtggcgcacagggtgatttgctgtgccgcgttgtcgtcgaaaca ccggtaggcctgaacgagaagcagaaacagctgctgcaagagctgcaagaaagcttcgg tggcccaaccggcgagcacaacagcccgcgctcaaagagcttctttgatggtgtgaaga agttttttgacgacctgacccgctaaaatcatgctctttctgtttt Proteins for Structural Studies • 527 completely sequenced genomes • > 5 million protein gene sequences, ~100,000 protein families, ~250,000 singletons • ~40-60% genes have a homologues with