A reference-grade wild soybean genome

Min Xie; Claire Yik Lok Chung; Man Wah Li; Fuk Ling Wong; Xin Wang; Ailin Liu; Zhili Wang; Alden King Yung Leung; Tin Hang Wong; Suk Wah Tong; Zhixia Xiao; Kejing Fan; Ming Sin Ng; Xinpeng Qi; Linfeng Yang; Tianquan Deng; Lijuan He; Lu Chen; Aisi Fu; Qiong Ding; Junxian He; Gyuhwa Chung; Sachiko Isobe; Takanari Tanabata; Babu Valliyodan; Henry T. Nguyen; Steven B. Cannon; Christine H. Foyer; Ting Fung Chan; Hon Ming Lam

doi:10.1038/s41467-019-09142-9

A reference-grade wild soybean genome

Min Xie, Claire Yik Lok Chung, Man Wah Li, Fuk Ling Wong, Xin Wang, Ailin Liu, Zhili Wang, Alden King Yung Leung, Tin Hang Wong, Suk Wah Tong, Zhixia Xiao, Kejing Fan, Ming Sin Ng, Xinpeng Qi, Linfeng Yang, Tianquan Deng, Lijuan He, Lu Chen, Aisi Fu, Qiong DingJunxian He, Gyuhwa Chung, Sachiko Isobe, Takanari Tanabata, Babu Valliyodan, Henry T. Nguyen, Steven B. Cannon, Christine H. Foyer, Ting Fung Chan^*, Hon Ming Lam

^*Corresponding author for this work

Life and Environmental Sciences

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Abstract

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.

Original language	English
Article number	1216
Number of pages	12
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-019-09142-9
Publication status	Published - 14 Mar 2019

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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Min_Xie_et_al_A_reference-grade_wild_soybean_genome_Nature_Communications_2019
Checked for eligibility: 02/09/2019
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title = "A reference-grade wild soybean genome",

abstract = "Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.",

author = "Min Xie and Chung, {Claire Yik Lok} and Li, {Man Wah} and Wong, {Fuk Ling} and Xin Wang and Ailin Liu and Zhili Wang and Leung, {Alden King Yung} and Wong, {Tin Hang} and Tong, {Suk Wah} and Zhixia Xiao and Kejing Fan and Ng, {Ming Sin} and Xinpeng Qi and Linfeng Yang and Tianquan Deng and Lijuan He and Lu Chen and Aisi Fu and Qiong Ding and Junxian He and Gyuhwa Chung and Sachiko Isobe and Takanari Tanabata and Babu Valliyodan and Nguyen, {Henry T.} and Cannon, {Steven B.} and Foyer, {Christine H.} and Chan, {Ting Fung} and Lam, {Hon Ming}",

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Xie, M, Chung, CYL, Li, MW, Wong, FL, Wang, X, Liu, A, Wang, Z, Leung, AKY, Wong, TH, Tong, SW, Xiao, Z, Fan, K, Ng, MS, Qi, X, Yang, L, Deng, T, He, L, Chen, L, Fu, A, Ding, Q, He, J, Chung, G, Isobe, S, Tanabata, T, Valliyodan, B, Nguyen, HT, Cannon, SB, Foyer, CH, Chan, TF & Lam, HM 2019, 'A reference-grade wild soybean genome', Nature Communications, vol. 10, no. 1, 1216. https://doi.org/10.1038/s41467-019-09142-9

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AU - Xie, Min

AU - Chung, Claire Yik Lok

AU - Li, Man Wah

AU - Wong, Fuk Ling

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AU - Wang, Zhili

AU - Leung, Alden King Yung

AU - Wong, Tin Hang

AU - Tong, Suk Wah

AU - Xiao, Zhixia

AU - Fan, Kejing

AU - Ng, Ming Sin

AU - Qi, Xinpeng

AU - Yang, Linfeng

AU - Deng, Tianquan

AU - He, Lijuan

AU - Chen, Lu

AU - Fu, Aisi

AU - Ding, Qiong

AU - He, Junxian

AU - Chung, Gyuhwa

AU - Isobe, Sachiko

AU - Tanabata, Takanari

AU - Valliyodan, Babu

AU - Nguyen, Henry T.

AU - Cannon, Steven B.

AU - Foyer, Christine H.

AU - Chan, Ting Fung

AU - Lam, Hon Ming

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AB - Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.

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JO - Nature Communications

JF - Nature Communications

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A reference-grade wild soybean genome

Abstract

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