title: De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
abstract: Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [4].
authors.forename: Ying-hui
authors.initials: YH
authors.lastname: Li
authors.affiliation: 1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] [3].
authors.forename: Guangyu
authors.initials: G
authors.lastname: Zhou
authors.affiliation: 1] Department of Agronomy, Purdue University, West Lafayette, Indiana, USA. [2].
authors.forename: Jianxin
authors.initials: J
authors.lastname: Ma
authors.affiliation: 1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2].
authors.forename: Wenkai
authors.initials: W
authors.lastname: Jiang
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Long-guo
authors.initials: LG
authors.lastname: Jin
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Zhouhao
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Jinbo
authors.initials: J
authors.lastname: Zhang
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Sui
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Liangtao
authors.initials: L
authors.lastname: Zheng
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Shan-shan
authors.initials: SS
authors.lastname: Zhang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Qiyang
authors.initials: Q
authors.lastname: Zuo
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Xue-hui
authors.initials: XH
authors.lastname: Shi
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Yan-fei
authors.initials: YF
authors.lastname: Li
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China.
authors.forename: Wan-ke
authors.initials: WK
authors.lastname: Zhang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Yiyao
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Guanyi
authors.initials: G
authors.lastname: Kong
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Hui-long
authors.initials: HL
authors.lastname: Hong
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Bing
authors.initials: B
authors.lastname: Tan
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Jian
authors.initials: J
authors.lastname: Song
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Zhang-xiong
authors.initials: ZX
authors.lastname: Liu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Yaoshen
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Hang
authors.initials: H
authors.lastname: Ruan
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Carol K L
authors.initials: CK
authors.lastname: Yeung
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Jian
authors.initials: J
authors.lastname: Liu
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Hailong
authors.initials: H
authors.lastname: Wang
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Li-juan
authors.initials: LJ
authors.lastname: Zhang
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Rong-xia
authors.initials: RX
authors.lastname: Guan
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Ke-jing
authors.initials: KJ
authors.lastname: Wang
authors.affiliation: Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, P.R. China.
authors.forename: Wen-bin
authors.initials: WB
authors.lastname: Li
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P.R. China.
authors.forename: Shou-yi
authors.initials: SY
authors.lastname: Chen
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Ru-zhen
authors.initials: RZ
authors.lastname: Chang
authors.affiliation: Novogene Bioinformatics Institute, Beijing, P.R. China.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: 1] Novogene Bioinformatics Institute, Beijing, P.R. China. [2] Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center, and School of Life Sciences, Peking University, Beijing, P.R. China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.affiliation: 1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
authors.forename: Li-juan
authors.initials: LJ
authors.lastname: Qiu
mesh_terms: D000383:Agriculture; D000595:Amino Acid Sequence; D018533:Biomass; D018744:DNA, Plant / Q000032:analysis / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012639:Seeds / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000145:classification / Q000235:genetics* / Q000502:physiology*
chemical_list: D018744:DNA, Plant