杨树泛基因组构建与基因组变异分析

储陈辰; 孙明升; 吴雨涵; 言震宇; 李婷; 冯洋帆; 国颖; 尹佟明; 薛良交

doi:10.12302/j.issn.1000-2006.202209037

杨树泛基因组构建与基因组变异分析

储陈辰, 孙明升, 吴雨涵, 言震宇, 李婷, 冯洋帆, 国颖, 尹佟明, 薛良交

南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (6) : 251-260.

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (6) : 251-260. DOI: 10.12302/j.issn.1000-2006.202209037

研究论文

杨树泛基因组构建与基因组变异分析

作者信息 +

Pan-genome and genomic variation analyses of Populus

Author information +

文章历史 +

摘要

【目的】杨树是重要的速生用材、生态防护和碳汇造林树种,也是林木遗传研究的模式树种。开展杨树泛基因组构建与基因组变异分析,可为杨树精准育种和林木泛基因组研究提供理论先导。【方法】以公开发表的高质量杨树基因组序列为基础,分析不同类型的序列变异,总结变异特征,并构建基于基因和图形结构的杨树泛基因组。【结果】本研究收集到8个杨属树种和3个二倍体或三倍体杨树杂交品种的基因组序列,3个杂交品种包含7个单倍型亚基因组序列,较好地代表了杨树4个组派的基因组特征。分析结果表明,杨树基因组间存在较多大的结构变异。在基于基因的泛基因组中,共线核心基因、非共线核心基因、次核心基因、非必需基因、特异基因占比分别为12.5%、34.9%、31.4%、16.5%、4.7%。其中,非必需基因在功能上具有较高的多样性。以基因组序列变异为基础构建杨树图形结构泛基因组,大幅提升2代测序数据的变异检测效果。通过泛基因组变异热点分析,鉴定出2个与物候关联的基因位点。【结论】杨属基因组中存在大量染色体重排,进而增加了基因调控的多样性。杨树组/派间的基因组结构变异可能与物候适应存在关联。基于林木基因组序列的复杂性,在林木泛基因组研究中应注意基因组整合范围与研究目标相匹配,结合基因泛基因组和图形结构泛基因组结果,综合解析林木的遗传变异规律和物种演化特征。

Abstract

【Objective】Poplar trees are important for timber production, ecological protection and carbon sequestration, and also serve as a model for forest genetic research. The construction of poplar pangenome and analysis of genomic variations will provide a theoretical guidance for poplar precision breeding and pan-genome research of forest trees. 【Method】All published high-quality poplar genome sequences were collected for a comparative genomic analysis. Both small genomic variations and large structural variations were identified and compared. Gene-based and graph-based pan-genomes were constructed, respectively. 【Result】Genomic sequences of eight poplar species and three diploid or triploid poplar hybrids were collected. The three hybrids contained seven haplotype subgenome sequences. These sequences represented the genomic characteristics of the four poplar Sections well. The comparative genomic analysis showed that there were many structural variations among poplar genomes. In the gene-based Populus pan-genomes, syntenic core genes, nonsyntenic core genes, softcore genes, dispensable genes, and private genes account for 12.5%, 34.9%, 31.4%, 16.5% and 4.7% of the total genes, respectively. Among them, dispensable genes exhibit a high functional diversity. Based on the variations of genome sequences, the graph-based poplar pangenome was constructed, which greatly improved the efficiency of variation detection using NGS data. Two genomic loci associated with phenology were identified through variation hotspot analysis of pan-genome. 【Conclusion】A large amount of genomic structural variations were observed in the genomes of Populus genus, which increase the diversity of gene regulation and thus affect the growth traits of poplar trees. The genomic structural variations among poplar Sections may be related to phenological adaptation. Due to the genomic complexity of forest trees, several aspects need to be considered during the construction of forest pangenomes, such as the agreement of included genomes and research objectives. The results from gene- and graph-based pan-genomes can be combined to explore the genomic variation and evolution of forest trees.

导出引用

储陈辰, 孙明升, 吴雨涵, 等. 杨树泛基因组构建与基因组变异分析[J]. 南京林业大学学报（自然科学版）. 2022, 46(6): 251-260 https://doi.org/10.12302/j.issn.1000-2006.202209037

CHU Chenchen, SUN Mingsheng, WU Yuhan, et al. Pan-genome and genomic variation analyses of Populus[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(6): 251-260 https://doi.org/10.12302/j.issn.1000-2006.202209037

中图分类号： S718

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