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Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics

文献类型： 外文期刊

作者： Yi, Xinxin 1 ; Liu, Jing 1 ; Chen, Shengcai 1 ; Wu, Hao 1 ; Liu, Min 1 ; Xu, Qing 1 ; Lei, Lingshan 1 ; Lee, Seunghee 1 ; Zhang, Bao 2 ; Kudrna, Dave 3 ; Fan, Wei 1 ; Wing, Rod A. 3 ; Wang, Xuelu 2 ; Zhang, Mengchen 1 ; Zhang, Jianwei 1 ; Yang, Chunyan 5 ; Chen, Nansheng 1 ;

作者机构： 1.Huazhong Agr Univ, Coll Life Sci & Technol, Ctr Integrat Biol, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Hubei, Peoples R China

2.Henan Univ, State Key Lab Crop Stress Adaptat & Improvement, Kaifeng 475004, Henan, Peoples R China

3.Univ Arizona, Arizona Genom Inst, Sch Plant Sci, Tucson, AZ 85721 USA

4.Univ Arizona, BIO5 Inst, Sch Plant Sci, Tucson, AZ 85721 USA

5.Hebei Acad Agr & Forestry Sci, Inst Food & Oil Crops, Shijiazhuang 050031, Hebei, Peoples R China

6.Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada

关键词： soybean cultivar Jidou 17; comparative genomics; symbiotic nitrogen fixation; assembly; genome

期刊名称：G3-GENES GENOMES GENETICS （ 影响因子：3.542； 五年影响因子：3.545 ）

ISSN： 2160-1836

年卷期： 2022 年 12 卷 4 期

页码：

收录情况： SCI

摘要： Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromosome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with 3 published soybeans (WM82, ZH13, and W05), which identified 5 large inversions and 2 large translocations specific to JD17, 20,984-46,912 presence-absence variations spanning 13.1-46.9 Mb in size. A total of 1,695,741-3,664,629 SNPs and 446,689-800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

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