基于33个遗传多样性水稻材料的泛基因组分析揭示“隐藏”的基因组变异

doi:10.16036/j.issn.1000-2650.2021.03.001

摘要/Abstract

摘要： 【目的】基因组结构变异(SV)和基因拷贝数变异(gCNV)是动植物中主要的遗传变异来源,全面准确地鉴定和分析 SV和gCNV对挖掘优异等位基因、保障水稻粮食安全具有重要意义。【方法】利用长片段测序数据和基因组装方法(HERA), 对31个具有遗传多样性的水稻栽培稻进行了高质量基因组组装,结合日本晴和蜀恢498高质量基因组,进行了系统的基因组比较分析。【结果】共鉴定到171 072个非冗余SVs和25549个gCNVs,其中82.8%的PAV未在先前基于短序列测序数据获得的PAV中鉴定到。利用非洲栽培稻CG14作为外群,对发生在亚洲栽培稻群体的SV(dSV)进行了推断,发现大多数dSV位于基因非编码区,以及泛基因组中50%(32668)基因上下游2kbp区域在32个亚洲栽培稻种至少有一个dSV。进一步结合转录组数据分析发现SVs和gCNVs对调控基因表达量对具有重要作用。对SV形成机制分析发现,SV主要由TEI(转座子插入)和NHEJ(非同源末端连接)两种机制形成,但不同类型SV的主要形成机制有所不同。该研究还构建了水稻中首个图形基因组,结合674份材料的二代测序和叶片早衰数据,发现17.5%的SV与其附近SNP的连锁度非常低,GWAS分析发现一个与叶片早衰显著相关的位点只能被SV检测到。相关研究成果以“Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations”为题于2021年5月发表在国际期刊Cell。【结论】提供了一个高质量泛基因组水平的基因组变异资源,将促进水稻的功能基因组和进化生物学研究、优异基因资源发掘和水稻育种。

关键词: 水稻, 泛基因组, 高质量基因组, 结构性变异, 基因拷贝数变异, 图形基因组

Abstract: 【Objective】 Structural variations (SVs) and gene copy number variation (gCNV) are a major source of genetic variation, identification and analysis of SV and gCNV is significant for mining elite natural allele and ensuring rice food security.【Method】 Using the long-read sequencing data and the method of genome assembly (HERA), we generated 31 high-quality assemblies of genetically diverse rice accessions. Coupling with Nipponbare and R498 high-quality genomes, we performed genomic sequence compar- isons and analysis.【Result】 We identified 171 072 non-redundant SVs and 25 549 gCNVs, and found that 82.8% of PAVs have not been discovered in previous study based on short-read sequencing. We used the O. glaberrima accession CG14 as an outgroup for inferring the SVs occurred in O. saliva (dSV), and found that a majority of dSVs shared overlap with non-coding region, also found that ~50%(32 668) of the genes in the pan-genome had at least one dSV overlapped with their region including +2 kbp of coding regions across the 32 O. saliva accessions. Coupling with analysis of transcriptome data, we found that SVs and gCNVs had significant roles in the regulation of gene expression. Analysis on the mechanism of SV formation found that most of these assigned SVs was formed through transposable element insertion (TEI) and nonhomologous end joining (NHEJ) (43.9%), but dominant mechanism was variable among different types of SV. This study also constructed a graph-based genome in rice. Coupling with the datasets of resequencing short-reads and leaf senescence phenotype of 674 accessions, we found that 17.5% of SVs showed very low linkage with nearby SNPs, and GWAS analysis showed that a locus significantly associated with leaf senescence phenotype was only detected using SV data. These related results was published in Cell in May 2021 titled ‘Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations’.【Conclusion】 Thisstudyprovideshigh-qualitypan-genome-scalegenomic variation resources, and will facilitate rice functional genomics and evolutionary biology research, elite natural allele mining and rice breeding.

Key words: rice, pan-genome, high-quality genome, structural variation, gene copy number variation, graph-based genome

中图分类号:

S511

钦鹏, 陈薇兰, 王淏, 李仕贵. 基于33个遗传多样性水稻材料的泛基因组分析揭示“隐藏”的基因组变异[J]. 四川农业大学学报, 2021, 39(3): 275-278.

QIN Peng, CHEN Weiion, WANG Hao, LI Shigui*. Pan-Genome Analysis of 33 Genetically Diverse Rice Accessions Reveals Hidden Genomic Variations[J]. Journal of Sichuan Agricultural University, 2021, 39(3): 275-278.

参考文献

[1] WEISCHENFELDT J, SYMMONS O, SPITZ F, et al. Phenotypic impact of genomic structural variation: insights from and for hu-man disease[J]. Nature Reviews Genetics, 2013, 14(2): 125-138.
[2] LYE Z N, PURUGGANAN M D.Copy Number variation in do-mestication[J]. Trends in Plant Science, 2019, 24(4): 352-365.
[3] SEDLAZECK F J, RESCHENEDER P, SMOLKA M, et al.Ac-curate detection of complex structural variations using single-molecule sequencing[J]. Nature Methods, 2018, 15(6): 461-468.
[4] HO S S, URBAN A E, MILLS R E.Structural variation in the sequencing era[J] Nature Reviews Genetics, 2020, 21(3): 171-189.
[5] ZHOU Y, MINIO A, MASSONNET M, et al. The population ge-netics of structural variants in grapevine domestication[J]. Nature Plants, 2019, 5(9): 965-979.
[6] YANG Z E, GE X Y, YANG Z R, et al.Extensive intraspecific gene order and gene structural variations in upland cotton culti-vars[J]. Nature Communications, 2019, 10: 2989.
[7] SUN S L, ZHOU Y S, CHEN J,et al.Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes[J]. Nature Genetics, 2018, 50(9): 1289-1295.
[8] WANG M,TU L,YUAN D, et al.Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense[J]. Nature Genetics, 2019, 51(2): 224-229.
[9] HUFNAGEL B, MARQUES A, SORIANO A, et al.High-quality genome sequence of white lupin provides insight into soil explo-ration and seed quality[J]. Nature Communications,2020, 11: 492.
[10] YANG N, LIU J, GAO Q, et al.Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement[J]. Nature Genetics, 2019, 51(6): 1052-1059.
[11] WANG W, MAULEON R, HU Z, et al.Genomic variation in 3010 diverse accessions of Asian cultivated rice[J]. Nature, 2018, 557(7703): 43-49.
[12] ZHAO Q,FENGQ, LU H, et al.Pan- genome analysis highlights the extent of genomic variation in cultivated and wild rice[J]. Na-ture Genetics, 2018, 50(2): 278-284.
[13] HU Z,WANG W, WU Z, et al.Novel sequences, structural variations and gene presence variations of Asian cultivated rice[J]. Scientific Data, 2018, 5: 180079.
[14] FUENTES R R, CHEBOTAROV D,DUITAMA J, et al.Struc-tural variants in 3 000 rice genomes[J]. Genome Research, 2019, 29(5): 870-880.
[15] SCHATZ M C, MARON L G, STEIN J C, et al.Whole genome de novo assemblies of three divergent strains of rice, Oryza sati-va, document novel gene space of aus and indica[J]. Genome Bi-ology, 2014, 15(11): 506.
[16] CARDOSO C, ZHANG Y, JAMIL M, et al.Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs[J]. Proceedings of the National Academy of Sciences, 2014, 111(6): 2379-2384.
[17] JEONG HJ, YANG J, CHO L H, et al.OsVIL1 controls flower-ing time in rice by suppressing OsLF under short days and by in-ducing Ghd7 under long days[J]. Plant Cell Reports, 2016, 35(4): 905-920.
[18] NONOUE Y, HORI K, ONO N, et al.Detection of heading date QTLs in advanced-backcross populations of an elite indica rice cultivar, R64[J]. Breed Science, 2019, 69(2): 352-358.
[19] YIN X,LIU X, XU B, et al.OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice[J]. Journal of Experimental Botany, 2019, 70(15): 3895-3909.
[20] QU S, LIU G, ZHOU B, et al.The broad-spectrum blast resis-tance gene Pi9 encodes a nucleotide -binding site -leucine -rich repeat protein and is a member of a multigene family in rice[J]. Genetics, 2006, 172(3): 1901-1914.