The future of legume genetic data resources: Challenges, opportunities, and priorities
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Ethalinda K. S. Cannon | Jacqueline D. Campbell | S. Cannon | N. Young | A. Chan | C. Town | J. Carlson | David Fernández-Baca | T. Close | P. Zhao | M. Monteros | M. Udvardi | K. Mysore | A. Farmer | S. Hokin | A. Cleary | A. Cooksey | C. Coyne | E. Wettberg | K. Bett | D. Cook | Connor T. Cameron | G. Bauchet | R. Dickstein | M. Muñoz‐Amatriaín | Yun Kang | E. Jones | C. Pislariu | S. Dash | A. Shi | Chris Richards | Connor Cameron | Alan M. Cleary | Catalina I. Pislariu
[1] Rajeev K. Varshney,et al. Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication , 2015, Proceedings of the National Academy of Sciences.
[2] Shuang-shuang Qin,et al. A draft genome for Spatholobus suberectus , 2019, Scientific Data.
[3] W. Scheible,et al. Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation , 2018 .
[4] Claire Yik-Lok Chung,et al. A reference-grade wild soybean genome , 2019, Nature Communications.
[5] K. Sjölander,et al. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). , 2006, Omics : a journal of integrative biology.
[6] Lukas A. Mueller,et al. solGS: a web-based tool for genomic selection , 2014, BMC Bioinformatics.
[7] James K. Hane,et al. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement , 2013, Nature Biotechnology.
[8] Juliane C. Dohm,et al. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes , 2016, Genome Biology.
[9] Y. van de Peer,et al. Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform1[W] , 2011, Plant Physiology.
[10] Shelby L. Bidwell,et al. An improved genome release (version Mt4.0) for the model legume Medicago truncatula , 2014, BMC Genomics.
[11] P. Cregan,et al. Fingerprinting Soybean Germplasm and Its Utility in Genomic Research , 2015, G3: Genes, Genomes, Genetics.
[12] Pierre Larmande,et al. Gigwa—Genotype investigator for genome-wide analyses , 2016, GigaScience.
[13] Jing Liu,et al. De novo assembly of a Chinese soybean genome , 2018, Science China Life Sciences.
[14] Steven L Salzberg,et al. Next-generation genome annotation: we still struggle to get it right , 2019, Genome Biology.
[15] Rod A Wing,et al. A reference genome for common bean and genome-wide analysis of dual domestications , 2014, Nature Genetics.
[16] Huanming Yang,et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers , 2011, Nature Biotechnology.
[17] Rachel S. Meyer,et al. Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. , 2012, The New phytologist.
[18] H. Liu,et al. Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement. , 2019, Molecular plant.
[19] P. Wincker,et al. A reference genome for pea provides insight into legume genome evolution , 2019, Nature Genetics.
[20] Justin N. Vaughn,et al. Development of the Alfalfa Breeder's Toolbox: Integration of Genomic, Genetic and Germplasm Resources for Alfalfa Improvement , 2018 .
[21] Robert M. Waterhouse,et al. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.
[22] Sergio Contrino,et al. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data , 2012, Bioinform..
[23] Hank C Wu,et al. Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. , 2007, The Plant journal : for cell and molecular biology.
[24] J. Schmutz,et al. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome , 2010, Proceedings of the National Academy of Sciences.
[25] Dave Kudrna,et al. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement , 2015, Scientific Reports.
[26] Rajeev K. Varshney,et al. Genome sequence of mungbean and insights into evolution within Vigna species , 2014, Nature Communications.
[27] Nevin D. Young,et al. Legumes as a Model Plant Family. Genomics for Food and Feed Report of the Cross-Legume Advances through Genomics Conference1 , 2005, Plant Physiology.
[28] S. Shu,et al. The genome of cowpea (Vigna unguiculata [L.] Walp.) , 2019, bioRxiv.
[29] D. K. Willis,et al. Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean , 2012, Science.
[30] Erez Lieberman Aiden,et al. The genome sequence of segmental allotetraploid peanut Arachis hypogaea , 2019, Nature Genetics.
[31] Kenneth L. McNally,et al. An imputation platform to enhance integration of rice genetic resources , 2018, Nature Communications.
[32] H. Mori,et al. Genome Structure of the Legume, Lotus japonicus , 2008, DNA research : an international journal for rapid publication of reports on genes and genomes.
[33] Sergio Contrino,et al. InterMine: extensive web services for modern biology , 2014, Nucleic Acids Res..
[34] Yves Van de Peer,et al. The draft genomes of five agriculturally important African orphan crops , 2018, GigaScience.
[35] Peng Zhou,et al. Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application) , 2013, BMC Bioinformatics.
[36] Matthias Lange,et al. Genebank genomics highlights the diversity of a global barley collection , 2018, Nature Genetics.
[37] C. N. Stewart,et al. Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes. , 2015, Molecular biology and evolution.
[38] Ruiqiang Li,et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits , 2014, Nature Biotechnology.
[39] A. Paterson,et al. Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform1[OPEN] , 2017, Plant Physiology.
[40] Bernhard Schölkopf,et al. easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies[OPEN] , 2016, Plant Cell.
[41] Uwe Scholz,et al. BrAPI—an application programming interface for plant breeding applications , 2019, Bioinform..
[42] Sanwen Huang,et al. Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor , 2019, Nature communications.
[43] The Computational Pan-Genomics Consortium,et al. Computational pan-genomics: status, promises and challenges , 2018, Briefings Bioinform..
[44] Michael K. Udvardi,et al. Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation1[OPEN] , 2017, Plant Physiology.
[45] S. Cannon,et al. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. , 2019, The New phytologist.
[46] Jason E. Stewart,et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.
[47] S. Cannon,et al. Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family , 2019, Front. Plant Sci..
[48] Huanming Yang,et al. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis , 2018, Science.
[49] Karsten M. Borgwardt,et al. The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog , 2017, Nucleic Acids Res..
[50] J. Miller,et al. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes , 2017, BMC Genomics.
[51] Kari Stefansson,et al. Graphtyper enables population-scale genotyping using pangenome graphs , 2017, Nature Genetics.
[52] Paul D. Shaw,et al. Flapjack—graphical genotype visualization , 2010, Bioinform..
[53] S. Isobe,et al. Draft genome sequence of subterranean clover, a reference for genus Trifolium , 2016, Scientific Reports.
[54] Michelle C. Stitzer,et al. Adaptation in plant genomes: Bigger is different. , 2018, American journal of botany.
[55] F. Arnaud,et al. From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory) , 2017 .
[56] Alvaro J. González,et al. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.
[57] S. Banniza,et al. Rapid generation cycling of an F2 population derived from a cross between Lens culinaris Medik. and Lens ervoides (Brign.) Grande after aphanomyces root rot selection , 2018, Plant Breeding.
[58] Claire Yik-Lok Chung,et al. Construction and comparison of three reference-quality genome assemblies for soybean. , 2019, The Plant journal : for cell and molecular biology.
[59] H. Kang,et al. Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells1[OPEN] , 2019, Plant Physiology.
[60] Andrew D. Farmer,et al. Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny , 2017, Bioinform..
[61] S. Ghimire,et al. The Mycorrhizal Fungus, Sebacina vermifera, Enhances Seed Germination and Biomass Production in Switchgrass (Panicum virgatum L) , 2009, BioEnergy Research.
[62] Mukesh Jain,et al. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.) , 2015, Scientific Reports.
[63] K. Nieselt,et al. Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing. , 2019, Developmental cell.
[64] S. Shu,et al. The genome of cowpea (Vigna unguiculata [L.] Walp.). , 2019, The Plant journal : for cell and molecular biology.
[65] S. Fields,et al. Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. , 2019, The Plant cell.
[66] Rajeev K. Varshney,et al. Draft genome sequence of adzuki bean, Vigna angularis , 2015, Scientific Reports.
[67] Xingtan Zhang,et al. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication , 2019, Nature Genetics.
[68] J. Gouzy,et al. Whole-genome landscape of Medicago truncatula symbiotic genes , 2018, Nature Plants.
[69] J. Eisen,et al. Research priorities for harnessing plant microbiomes in sustainable agriculture , 2017, PLoS biology.
[70] Rafael Barbosa Pinto,et al. A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny , 2017 .
[71] J. Joets,et al. OptiMAS: A Decision Support Tool for Marker-Assisted Assembly of Diverse Alleles , 2013, The Journal of heredity.
[72] S. Cannon,et al. Legumes as a model plant family , 2011 .
[73] Ying Zhang,et al. Computational pan-genomics: status, promises and challenges , 2016, bioRxiv.
[74] H. Steinberg,et al. Spectroscopy of bulk and few-layer superconducting NbSe2 with van der Waals tunnel junctions , 2017, Nature Communications.
[75] Uwe Scholz,et al. Measures for interoperability of phenotypic data: minimum information requirements and formatting , 2016, Plant Methods.
[76] Lukas A. Mueller,et al. The Sol Genomics Network (SGN)—from genotype to phenotype to breeding , 2014, Nucleic Acids Res..
[77] H. Kanamori,et al. The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars , 2015, International journal of genomics.
[78] K. Vandepoele,et al. Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences[OPEN] , 2016, Plant Cell.
[79] G. Hartman,et al. Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean. , 2018, The Plant journal : for cell and molecular biology.
[80] Y. Li,et al. Legume Crops Phylogeny and Genetic Diversity for Science and Breeding , 2015 .
[81] Z. Fei,et al. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor , 2019, Nature Genetics.
[82] M. Purugganan,et al. Copy Number Variation in Domestication. , 2019, Trends in plant science.
[83] Barry Smith,et al. The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species , 2019, Front. Plant Sci..
[84] Stephen P. Ficklin,et al. Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases , 2013, Database J. Biol. Databases Curation.
[85] Melanie Kappelmann-Fenzl. Reference Genome , 2021, Next Generation Sequencing and Data Analysis.
[86] Rachael L. Ashby,et al. Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover. , 2019, The Plant cell.
[87] Stephen P. Ficklin,et al. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture , 2018, Database J. Biol. Databases Curation.
[88] Wei Huang,et al. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut , 2016, Nature Genetics.
[89] K. Sahu,et al. Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.
[90] Karsten M. Borgwardt,et al. AraPheno: a public database for Arabidopsis thaliana phenotypes , 2016, Nucleic Acids Res..
[91] Matthias Lange,et al. Towards recommendations for metadata and data handling in plant phenotyping. , 2015, Journal of experimental botany.
[92] Jesse Poland,et al. Field Book: An Open‐Source Application for Field Data Collection on Android , 2014 .
[93] Hiroaki Sakai,et al. The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome , 2015, Scientific Reports.
[94] Erik Schultes,et al. The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.
[95] N. Morrison,et al. Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature , 2010, AoB PLANTS.
[96] S. Udupa,et al. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria , 2019, Proceedings of the National Academy of Sciences.
[97] P. L. Chang,et al. Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation , 2018, Nature Communications.
[98] T. Sakurai,et al. Genome sequence of the palaeopolyploid soybean , 2010, Nature.
[99] James K. Hane,et al. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution , 2016, Plant biotechnology journal.
[100] Trevor W. Rife. Field Book: An Open-Source Application for Phenotypic Data Collection on Android , 2014 .
[101] E. V. von Wettberg,et al. The Impact of Genetic Changes during Crop Domestication , 2018, Agronomy.