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Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes

文献类型： 外文期刊

作者： Ni, Lingbin 1 ; Liu, Yucheng 1 ; Ma, Xin 1 ; Liu, Tengfei 1 ; Yang, Xiaoyue 1 ; Wang, Zhao 1 ; Liang, Qianjin 1 ; Liu, Shulin 1 ; Zhang, Min 1 ; Wang, Zheng 3 ; Shen, Yanting 1 ; Tian, Zhixi 1 ;

作者机构： 1.Chinese Acad Sci, Inst Genet & Dev Biol, Innovat Acad Seed Design, State Key Lab Plant Cell & Chromosome Engn, Beijing 100101, Peoples R China

2.Univ Chinese Acad Sci, Coll Adv Agr Sci, Beijing 100049, Peoples R China

3.Beijing Acad Agr & Forestry Sci, Beijing Vegetable Res Ctr, Beijing Key Lab Vegetable Germplasm Improvement, Beijing 100097, Peoples R China

关键词： Pan-3D genome; Structural variations; Non-LTR retrotransposons; Gypsy elements; Satellite repeats; PAV

期刊名称：GENOME BIOLOGY （ 影响因子：12.3； 五年影响因子：17.4 ）

ISSN： 1474-760X

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundHigh-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.ResultsHere, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication.ConclusionOur study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.

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