Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Espina, Mary C.; Lovell, John T.; Jenkins, Jerry; Shu, Shengqiang; Sreedasyam, Avinash; Jordan, Brandon D.; Webber, Jenell; Boston, LoriBeth; Brůna, Tomáš; Talag, Jayson; Goodstein, David; Grimwood, Jane; Stacey, Gary; Cannon, Steven B.; Lorenz, Aaron J.; Schmutz, Jeremy; Stupar, Robert M.

doi:10.1111/tpj.17026

Title: Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Journal Article · Sat Sep 14 00:00:00 UTC 2024 · The Plant Journal

DOI: https://doi.org/10.1111/tpj.17026 · OSTI ID:2498349

Espina, Mary C. ^[1]; Lovell, John T. ^[2]; Jenkins, Jerry ^[3]; Shu, Shengqiang ^[4];

^[2]; Jordan, Brandon D. ^[5]; Webber, Jenell ^[3]; Boston, LoriBeth ^[3]; Brůna, Tomáš ^[4]; Talag, Jayson ^[6]; Goodstein, David ^[4]; Grimwood, Jane ^[3];

^[7]; Cannon, Steven B. ^[5]; Lorenz, Aaron J. ^[1];

^[2];

^[1]

University of Minnesota, Saint Paul, MN (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
US Dept. of Agriculture (USDA), Ames, IA (United States). Agricultural Research Service (ARS)
Univ. of Arizona, Tucson, AZ (United States)
Univ. of Missouri, Columbia, MO (United States)

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-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (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 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (> 20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two near-gapless 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 ‘Fiskeby III,’ 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2498349

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 3 Vol. 120; ISSN 0960-7412

Publisher:: Society for Experimental BiologyCopyright Statement

Country of Publication:: United States

Language:: English

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