{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T23:32:52Z","timestamp":1792193572289,"version":"4.4.0"},"reference-count":45,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2024,9,14]],"date-time":"2024-09-14T00:00:00Z","timestamp":1726272000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","award":["0201\u201088888\u2010002\u2010000D"],"award-info":[{"award-number":["0201\u201088888\u2010002\u2010000D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","award":["0201\u201088888\u2010003\u2010000D"],"award-info":[{"award-number":["0201\u201088888\u2010003\u2010000D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","award":["5030\u201021000\u2010071\u2010000D"],"award-info":[{"award-number":["5030\u201021000\u2010071\u2010000D"]}],"id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015911","name":"Joint Genome Institute","doi-asserted-by":"publisher","award":["DE\u2010AC02\u201005CH11231"],"award-info":[{"award-number":["DE\u2010AC02\u201005CH11231"]}],"id":[{"id":"10.13039\/100015911","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012009","name":"United Soybean Board","doi-asserted-by":"publisher","award":["1920\u2010172\u20100116\u2010C"],"award-info":[{"award-number":["1920\u2010172\u20100116\u2010C"]}],"id":[{"id":"10.13039\/100012009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012009","name":"United Soybean Board","doi-asserted-by":"publisher","award":["2311\u2010209\u20100501"],"award-info":[{"award-number":["2311\u2010209\u20100501"]}],"id":[{"id":"10.13039\/100012009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2022\u201067013\u201036128"],"award-info":[{"award-number":["2022\u201067013\u201036128"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Journal"],"published-print":{"date-parts":[[2024,11]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                  <jats:p>Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub\u2010lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub\u2010line known as Wm82\u2010ISU\u201001 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48\u2009387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near\u2010gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30\u2009Mb and 25\u2009Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (&gt;20\u2009Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the \u2018Williams\u2019 haplotype while the other two near\u2010gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of \u2018Fiskeby III,\u2019 a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.<\/jats:p>","DOI":"10.1111\/tpj.17026","type":"journal-article","created":{"date-parts":[[2024,9,14]],"date-time":"2024-09-14T13:58:51Z","timestamp":1726322331000},"page":"1221-1235","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean"],"prefix":"10.1111","volume":"120","author":[{"given":"Mary Jane C.","family":"Espina","sequence":"first","affiliation":[{"name":"Department of Agronomy and Plant Genetics University of Minnesota  St. Paul Minnesota 55108 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John T.","family":"Lovell","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"},{"name":"Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute  Berkeley California 94720 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerry","family":"Jenkins","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengqiang","family":"Shu","sequence":"additional","affiliation":[{"name":"Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute  Berkeley California 94720 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7336-7012","authenticated-orcid":false,"given":"Avinash","family":"Sreedasyam","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"},{"name":"Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute  Berkeley California 94720 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon D.","family":"Jordan","sequence":"additional","affiliation":[{"name":"Corn Insects and Crop Genetics Research Unit, US Department of Agriculture \u2013 Agricultural Research Service  Ames Iowa 50011 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenell","family":"Webber","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"LoriBeth","family":"Boston","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom\u00e1\u0161","family":"Br\u016fna","sequence":"additional","affiliation":[{"name":"Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute  Berkeley California 94720 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayson","family":"Talag","sequence":"additional","affiliation":[{"name":"Arizona Genomics Institute, School of Plant Sciences, University of Arizona  Tucson Arizona 85721 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Goodstein","sequence":"additional","affiliation":[{"name":"Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute  Berkeley California 94720 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Grimwood","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5914-2247","authenticated-orcid":false,"given":"Gary","family":"Stacey","sequence":"additional","affiliation":[{"name":"Division of Plant Science &amp; Technology, C.S. Bond Life Sciences Center University of Missouri  Columbia Missouri 65211 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven B.","family":"Cannon","sequence":"additional","affiliation":[{"name":"Corn Insects and Crop Genetics Research Unit, US Department of Agriculture \u2013 Agricultural Research Service  Ames Iowa 50011 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron J.","family":"Lorenz","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Plant Genetics University of Minnesota  St. Paul Minnesota 55108 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8062-9172","authenticated-orcid":false,"given":"Jeremy","family":"Schmutz","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology  Huntsville Alabama 35806 USA"},{"name":"Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute  Berkeley California 94720 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8836-2924","authenticated-orcid":false,"given":"Robert M.","family":"Stupar","sequence":"additional","affiliation":[{"name":"Department of Agronomy and Plant Genetics University of Minnesota  St. Paul Minnesota 55108 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,9,14]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003\u2010021\u201002559\u20103"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci1988.0011183X002800060049x"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010016\u20102687\u20101"},{"key":"e_1_2_9_5_1","volume-title":"QTL mapping and GWAS identify sources of iron deficiency chlorosis and canopy wilt tolerance in the Fiskeby III x Mandarin (Ottawa) soybean population","author":"Butenhoff K.","year":"2015"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010023\u201009161\u20103"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588\u2010023\u201001419\u20106"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2022.06.010"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010017\u20103015\u20100"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci2005.09.0334"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20382"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.109.137935"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2022.102886"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg770"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.110.166736"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2023.08.007"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.05.023"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.78526"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.323"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.3835\/plantgenome2019.01.0007"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1002\/csc2.20661"},{"key":"e_1_2_9_26_1","volume-title":"Fine\u2010mapping, physiological evaluation, and candidate gene exploration of an iron deficiency chlorosis tolerance locus in soybean","author":"Merry R.A.","year":"2020"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20000"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.13816"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20153837"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.10.4.516"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08670"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.2135\/cropsci2009.02.0078"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u20106\u201031"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0054985"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010015\u20102344\u20100"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad616"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1111\/pbi.13600"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1007\/s001220050654"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41597\u2010021\u201000834\u2010w"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.14500"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbi.2019.12.004"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gpb.2021.08.003"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2023.08.012"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq057"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.48130\/TP\u20102022\u20100007"}],"container-title":["The Plant Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tpj.17026","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tpj.17026","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,30]],"date-time":"2024-10-30T13:16:03Z","timestamp":1730294163000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.17026"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,14]]},"references-count":45,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,11]]}},"alternative-id":["10.1111\/tpj.17026"],"URL":"https:\/\/doi.org\/10.1111\/tpj.17026","archive":["Portico"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.04.26.591401","asserted-by":"object"}]},"ISSN":["0960-7412","1365-313X"],"issn-type":[{"value":"0960-7412","type":"print"},{"value":"1365-313X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,14]]},"assertion":[{"value":"2024-05-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-08-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-09-14","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}