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Title: Construction and comparison of three reference-quality genome assemblies for soybean

Abstract

Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. Themore » genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.« less

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [2];  [5];  [6];  [7];  [7];  [4];  [6];  [8];  [9];  [4];  [5];  [10]; ORCiD logo [11];  [3];  [3];  [12] more »;  [13];  [14];  [4];  [10];  [7]; ORCiD logo [15]; ORCiD logo [6];  [6];  [3]; ORCiD logo [10] « less
  1. Univ. of Missouri, Columbia, MO (United States); Lincoln Univ., Jefferson City, MO (United States)
  2. US Dept. of Agriculture (USDA)., Ames, IA (United States)
  3. The Univ. of Western Australia, Crawley, WA (Australia)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Iowa State Univ., Ames, IA (United States)
  6. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  7. Chinese Univ. of Hong Kong (China)
  8. Bionano Genomics, San Diego, CA (United States)
  9. NRGene Ltd., Ness Ziona (Israel)
  10. Univ. of Missouri, Columbia, MO (United States)
  11. International Crops Research Inst. for the Semi‐Arid Tropics (ICRISAT), Patancheru (India)
  12. School of Biological Sciences The University of Western Australia Crawley 6009 WA Australia
  13. US Dept. of Agriculture (USDA)., Beltsville, MD (United States)
  14. Univ. of Minnesota, St. Paul, MN (United States)
  15. Univ. of Georgia, Athens, GA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF); USDA
OSTI Identifier:
1619141
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 100; Journal Issue: 5; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; glycine max; glycine soja; soybean; genome assembly; domestication; comparative genomics

Citation Formats

Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y. ‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, and Nguyen, Henry T.. Construction and comparison of three reference-quality genome assemblies for soybean. United States: N. p., 2019. Web. https://doi.org/10.1111/tpj.14500.
Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y. ‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, & Nguyen, Henry T.. Construction and comparison of three reference-quality genome assemblies for soybean. United States. https://doi.org/10.1111/tpj.14500
Valliyodan, Babu, Cannon, Steven B., Bayer, Philipp E., Shu, Shengqiang, Brown, Anne V., Ren, Longhui, Jenkins, Jerry, Chung, Claire Y. ‐L., Chan, Ting‐Fung, Daum, Christopher G., Plott, Christopher, Hastie, Alex, Baruch, Kobi, Barry, Kerrie W., Huang, Wei, Patil, Gunvant, Varshney, Rajeev K., Hu, Haifei, Batley, Jacqueline, Yuan, Yuxuan, Song, Qijian, Stupar, Robert M., Goodstein, David M., Stacey, Gary, Lam, Hon‐Ming, Jackson, Scott A., Schmutz, Jeremy, Grimwood, Jane, Edwards, David, and Nguyen, Henry T.. Wed . "Construction and comparison of three reference-quality genome assemblies for soybean". United States. https://doi.org/10.1111/tpj.14500. https://www.osti.gov/servlets/purl/1619141.
@article{osti_1619141,
title = {Construction and comparison of three reference-quality genome assemblies for soybean},
author = {Valliyodan, Babu and Cannon, Steven B. and Bayer, Philipp E. and Shu, Shengqiang and Brown, Anne V. and Ren, Longhui and Jenkins, Jerry and Chung, Claire Y. ‐L. and Chan, Ting‐Fung and Daum, Christopher G. and Plott, Christopher and Hastie, Alex and Baruch, Kobi and Barry, Kerrie W. and Huang, Wei and Patil, Gunvant and Varshney, Rajeev K. and Hu, Haifei and Batley, Jacqueline and Yuan, Yuxuan and Song, Qijian and Stupar, Robert M. and Goodstein, David M. and Stacey, Gary and Lam, Hon‐Ming and Jackson, Scott A. and Schmutz, Jeremy and Grimwood, Jane and Edwards, David and Nguyen, Henry T.},
abstractNote = {Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.},
doi = {10.1111/tpj.14500},
journal = {The Plant Journal},
number = 5,
volume = 100,
place = {United States},
year = {2019},
month = {8}
}

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Works referenced in this record:

Versatile and open software for comparing large genomes
journal, January 2004

  • Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
  • Genome Biology, Vol. 5, Issue 2, R12
  • DOI: 10.1186/gb-2004-5-2-r12

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
journal, February 2015

  • Zhou, Zhengkui; Jiang, Yu; Wang, Zheng
  • Nature Biotechnology, Vol. 33, Issue 4
  • DOI: 10.1038/nbt.3096

The UCSC genome browser and associated tools
journal, August 2012

  • Kuhn, R. M.; Haussler, D.; Kent, W. J.
  • Briefings in Bioinformatics, Vol. 14, Issue 2
  • DOI: 10.1093/bib/bbs038

A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants
journal, March 2016

  • Bergelson, Joy; Buckler, Edward S.; Ecker, Joseph R.
  • The Plant Cell, Vol. 28, Issue 3
  • DOI: 10.1105/tpc.15.00502

Impacts of genetic bottlenecks on soybean genome diversity
journal, October 2006

  • Hyten, D. L.; Song, Q.; Zhu, Y.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 45
  • DOI: 10.1073/pnas.0604379103

Ab initio Gene Finding in Drosophila Genomic DNA
journal, April 2000

  • Salamov, Asaf A.; Solovyev, Victor V.
  • Genome Research, Vol. 10, Issue 4, p. 516-522
  • DOI: 10.1101/gr.10.4.516

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82
journal, November 2010

  • Haun, William J.; Hyten, David L.; Xu, Wayne W.
  • Plant Physiology, Vol. 155, Issue 2
  • DOI: 10.1104/pp.110.166736

A reference-grade wild soybean genome
journal, March 2019


KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences
journal, September 2017

  • Laetsch, Dominik R.; Blaxter, Mark L.
  • G3: Genes|Genomes|Genetics, Vol. 7, Issue 10
  • DOI: 10.1534/g3.117.300233

Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats
journal, October 2009

  • Tuteja, Jigyasa H.; Zabala, Gracia; Varala, Kranthi
  • The Plant Cell, Vol. 21, Issue 10
  • DOI: 10.1105/tpc.109.069856

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean
journal, November 2012


The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations
journal, September 2014

  • Vaughn, Justin N.; Nelson, Randall L.; Song, Qijian
  • G3: Genes|Genomes|Genetics, Vol. 4, Issue 11
  • DOI: 10.1534/g3.114.013433

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015


Registration of ‘Corsoy 79’ Soybean
journal, November 1988


FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Molecular basis of a shattering resistance boosting global dissemination of soybean
journal, December 2014

  • Funatsuki, Hideyuki; Suzuki, Masaya; Hirose, Aya
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 50
  • DOI: 10.1073/pnas.1417282111

Genome sequence of the palaeopolyploid soybean
journal, January 2010

  • Schmutz, Jeremy; Cannon, Steven B.; Schlueter, Jessica
  • Nature, Vol. 463, Issue 7278
  • DOI: 10.1038/nature08670

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
journal, November 2013

  • Burton, Joshua N.; Adey, Andrew; Patwardhan, Rupali P.
  • Nature Biotechnology, Vol. 31, Issue 12
  • DOI: 10.1038/nbt.2727

A Fluorescence in Situ Hybridization System for Karyotyping Soybean
journal, April 2010


Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus
journal, October 2004

  • Clough, Steven J.; Tuteja, Jigyasa H.; Li, Min
  • Genome, Vol. 47, Issue 5
  • DOI: 10.1139/g04-049

Pod shattering resistance associated with domestication is mediated by a NAC gene in soybean
journal, February 2014

  • Dong, Yang; Yang, Xia; Liu, Jing
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4352

Inheritance of Salt Tolerance in Wild Soybean (Glycine soja Sieb. and Zucc.) Accession PI483463
journal, May 2009

  • Lee, J. -D.; Shannon, J. G.; Vuong, T. D.
  • Journal of Heredity, Vol. 100, Issue 6
  • DOI: 10.1093/jhered/esp027

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants
journal, November 2016


Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform
journal, March 2017

  • Wang, Jinpeng; Sun, Pengchuan; Li, Yuxian
  • Plant Physiology, Vol. 174, Issue 1
  • DOI: 10.1104/pp.16.01981

phyloXML: XML for evolutionary biology and comparative genomics
journal, October 2009


InterProScan 5: genome-scale protein function classification
journal, January 2014


Towards plant pangenomics
journal, November 2015

  • Golicz, Agnieszka A.; Batley, Jacqueline; Edwards, David
  • Plant Biotechnology Journal, Vol. 14, Issue 4
  • DOI: 10.1111/pbi.12499

Fine mapping of a major quantitative trait locus that regulates pod shattering in soybean
journal, April 2013


Genomic selection: genome-wide prediction in plant improvement
journal, September 2014


BLAT---The BLAST-Like Alignment Tool
journal, March 2002


Preparation and flow cytometric analysis of metaphase chromosomes of tomato
journal, July 1991

  • Arumuganathan, K.; Slattery, J. P.; Tanksley, S. D.
  • Theoretical and Applied Genetics, Vol. 82, Issue 1
  • DOI: 10.1007/BF00231283

Evaluation of Soybean Differentials for Their Interaction with Phytophthora sojae
journal, January 2004


The Glycine max cv. Enrei Genome for Improvement of Japanese Soybean Cultivars
journal, January 2015

  • Shimomura, Michihiko; Kanamori, Hiroyuki; Komatsu, Setsuko
  • International Journal of Genomics, Vol. 2015
  • DOI: 10.1155/2015/358127

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
journal, January 2012

  • Wang, Y.; Tang, H.; DeBarry, J. D.
  • Nucleic Acids Research, Vol. 40, Issue 7
  • DOI: 10.1093/nar/gkr1293

VSEARCH: a versatile open source tool for metagenomics
journal, January 2016


Artificial selection for determinate growth habit in soybean
journal, April 2010

  • Tian, Z.; Wang, X.; Lee, R.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 19
  • DOI: 10.1073/pnas.1000088107

A high-performance computing toolset for relatedness and principal component analysis of SNP data
journal, October 2012


Fingerprinting Soybean Germplasm and Its Utility in Genomic Research
journal, July 2015

  • Song, Qijian; Hyten, David L.; Jia, Gaofeng
  • G3: Genes|Genomes|Genetics, Vol. 5, Issue 10
  • DOI: 10.1534/g3.115.019000

SoyTEdb: a comprehensive database of transposable elements in the soybean genome
journal, January 2010


Chromosome Visualization Tool: A Whole Genome Viewer
journal, January 2011

  • Cannon, Ethalinda K. S.; Cannon, Steven B.
  • International Journal of Plant Genomics, Vol. 2011
  • DOI: 10.1155/2011/373875

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
journal, September 2014

  • Li, Ying-hui; Zhou, Guangyu; Ma, Jianxin
  • Nature Biotechnology, Vol. 32, Issue 10
  • DOI: 10.1038/nbt.2979

CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula
journal, December 2017

  • Curtin, Shaun J.; Xiong, Yer; Michno, Jean-Michel
  • Plant Biotechnology Journal, Vol. 16, Issue 6
  • DOI: 10.1111/pbi.12857

Tissue-Specific Gene Silencing Mediated by a Naturally Occurring Chalcone Synthase Gene Cluster in Glycine max
journal, April 2004

  • Tuteja, Jigyasa H.; Clough, Steven J.; Chan, Wan-Ching
  • The Plant Cell, Vol. 16, Issue 4
  • DOI: 10.1105/tpc.021352

BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
journal, March 2007


Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01
journal, January 2016


Improved maize reference genome with single-molecule technologies
journal, June 2017

  • Jiao, Yinping; Peluso, Paul; Shi, Jinghua
  • Nature, Vol. 546, Issue 7659
  • DOI: 10.1038/nature22971

A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection
journal, November 2015


Molecular and Chromosomal Evidence for Allopolyploidy in Soybean
journal, July 2009

  • Gill, Navdeep; Findley, Seth; Walling, Jason G.
  • Plant Physiology, Vol. 151, Issue 3
  • DOI: 10.1104/pp.109.137935

A genome-wide association study of seed protein and oil content in soybean
journal, January 2014


Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max
journal, March 2017

  • Cho, Young B.; Jones, Sarah I.; Vodkin, Lila O.
  • The Plant Cell, Vol. 29, Issue 4
  • DOI: 10.1105/tpc.17.00162

Soybean domestication: the origin, genetic architecture and molecular bases
journal, January 2017

  • Sedivy, Eric J.; Wu, Faqiang; Hanzawa, Yoshie
  • New Phytologist, Vol. 214, Issue 2
  • DOI: 10.1111/nph.14418

GMAP: a genomic mapping and alignment program for mRNA and EST sequences
journal, February 2005


Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
journal, October 2003


Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean
journal, January 2013


GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean
journal, June 2015

  • Sun, Lianjun; Miao, Zhenyan; Cai, Chunmei
  • Nature Genetics, Vol. 47, Issue 8
  • DOI: 10.1038/ng.3339

Pfam: the protein families database
journal, November 2013

  • Finn, Robert D.; Bateman, Alex; Clements, Jody
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1223

Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon
journal, March 2010


Chalcone Synthase mRNA and Activity Are Reduced in Yellow Soybean Seed Coats with Dominant I Alleles
journal, June 1994

  • Wang, C. S.; Todd, J. J.; Vodkin, L. O.
  • Plant Physiology, Vol. 105, Issue 2
  • DOI: 10.1104/pp.105.2.739

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication
journal, July 2017


The Rosa genome provides new insights into the domestication of modern roses
journal, April 2018


Assembly and comparison of two closely related Brassica napus genomes
journal, June 2017

  • Bayer, Philipp E.; Hurgobin, Bhavna; Golicz, Agnieszka A.
  • Plant Biotechnology Journal, Vol. 15, Issue 12
  • DOI: 10.1111/pbi.12742

Genome sequence of the progenitor of wheat A subgenome Triticum urartu
journal, May 2018


Assembly and annotation of a draft genome sequence for Glycine latifolia , a perennial wild relative of soybean
journal, May 2018

  • Liu, Qiong; Chang, Sungyul; Hartman, Glen L.
  • The Plant Journal, Vol. 95, Issue 1
  • DOI: 10.1111/tpj.13931

De novo assembly of a Chinese soybean genome
journal, July 2018


The maize W22 genome provides a foundation for functional genomics and transposon biology
journal, July 2018

  • Springer, Nathan M.; Anderson, Sarah N.; Andorf, Carson M.
  • Nature Genetics, Vol. 50, Issue 9
  • DOI: 10.1038/s41588-018-0158-0

BLAT---The BLAST-Like Alignment Tool
journal, March 2002


    Works referencing / citing this record:

    The future of legume genetic data resources: Challenges, opportunities, and priorities
    journal, November 2019

    • Bauchet, Guillaume J.; Bett, Kirstin E.; Cameron, Connor T.
    • Legume Science, Vol. 1, Issue 1
    • DOI: 10.1002/leg3.16