基于全基因组重测序的泡桐属植物遗传关系分析

Genetic relationship analysis of Paulownia species using whole genome re-sequencing

【目的】基于全基因组重测序技术(WGRS)开发的SNP标记,对泡桐属的种间亲缘关系和群体遗传结构进行解析,为揭示泡桐属植物的系统发育关系及进行分类提供理论依据。【方法】对泡桐属11个桐种的典型株进行全基因组重测序,评估数据质量;以白花泡桐基因组为参考,获得高质量SNP位点,并进一步通过VCF2Dis、MEGA11和fast STRUCTURE等软件对其进行主成分分析(PCA)、系统发育分析和群体遗传结构分析;采用cluster Profiler包对基因进行富集分析。【结果】通过WGRS技术对泡桐属11个桐种的典型株进行测序,11份材料比对至白花泡桐参考基因组的平均比对率为81.87%,通过有效过滤筛选后获得7 492 966个SNP位点。基于这些SNP位点估算材料间的遗传距离,种间的遗传距离为0.15~0.59,毛泡桐与白花泡桐的遗传距离最大为0.59,宜昌泡桐与山明泡桐,鄂川泡桐与山明泡桐的遗传距离最小,均为0.15。PCA、系统发育树和遗传结构分析结果均将泡桐属划分为3个类群,类群Ⅰ为毛泡桐;类群Ⅱ包括川泡桐和台湾泡桐;类群Ⅲ包括白花泡桐、楸叶泡桐、山明泡桐、鄂川泡桐、宜昌泡桐、华东泡桐、建始泡桐和兰考泡桐。高突变率基因被富集到细胞壁代谢、花粉代谢、次生代谢物代谢和形态建成相关的生物学过程。【结论】利用WGRS技术挖掘覆盖全基因组的SNP标记可以有效地对泡桐属植物的亲缘关系及遗传结构进行解析,为泡桐属种质资源的系统分类和高效利用奠定基础。

【Objective】Based on the SNP markers developed by whole genome re-sequencing,the genetic relationship and population genetic structure of Paulownia species were analyzed,which will provide a theoretical basis for reveling the phylogenetic relationship and classification of Paulownia species.【Method】11 species of Paulownia were sequenced using WGRS,and the basic quality and characteristics of the obtained data were evaluated.Using the whole genome sequence of Paulownia fortunei as the reference genome,the SNP markers with high quality were obtained.Principle component analysis(PCA)and the phylogenetic and genetic structure of these species were analyzed through VCF2Dis,MEGA11 and fastSTRUCTURE and other software.GO enrichment analysis was performed by the R package of cluster Profiler.【Result】81.87%of the reads were mapped to the P.fortunei genome,and 7492966 SNPs were obtained after cleaning and filtering.Based on these SNPs,the genetic distance between each of the two species was estimated.The genetic distance ranged from 0.15 to 0.59,among which the distance between P.tomentosa and P.fortunei was the largest at 0.59,the distance between P.ichangensis and P.lampropylla,and the distance between P.albiphloea and P.lampropylla were the smallest as 0.15.The results of phylogenetic analysis,PCA,and genetic structure analysis confirmed that 11 species of Paulownia should be classified into 3 groups,which were the group of P.tomentosa(Ⅰ),the group of P.fargesii and P.taiwaniana(Ⅱ)and the group of P.fortunei,P.catalpifolia,P.lampropylla,P.albiphloea,P.ichangensis,P.kawakamii,P.jianshiensis and P.elonga(Ⅲ).Genes with high mutation rates were enriched to the cell wall-related pathway,pollen-related pathway,secondary metabolite-related pathway and morphogenesis-related pathway.【Conclusion】Using the WGRS technique to mine the SNP markers covering the whole genome,the genetic diversity and genetic structure of Paulownia species could be analyzed effectively.It lays a foundation for the systematic classification and efficient utilization of Paulownia germplasm resources.