川芎基因组survey测序及其特征分析

Genome survey and characteristic analysis of Ligusticum chuanxiong

目的利用流式细胞术和高通量测序技术,对川芎Ligusticum chuanxiong基因组大小和特征进行分析,为川芎全基因组精细测序和分子机制研究奠定基础。方法以已知基因组大小的绿豆和陆地棉作为内标植物,用流式细胞术估算川芎基因组大小。利用高通量测序技术对川芎基因组进行survey分析,测算出川芎基因组大小、重复序列、杂合率和GC含量等,利用生物信息学对基因组进行预测、注释和基因家族鉴定。结果估算出川芎基因组大小约为3058.37Mb,重复序列为79.79%,杂合率约2.16%,GC含量为36.32%,川芎基因组呈现高重复、高杂合、基因组庞大等特征。共预测到34864个基因,有30737个基因在功能数据库中被注释,有53个基因注释到阿魏酸合成过程中。初步鉴定到2058个特异基因家族,2001个单拷贝基因。结论初步获得了川芎基因组大小、基因组特征、功能基因及基因家族等信息,为进一步川芎全基因组精细测序提供了参考,为阐明川芎阿魏酸等药效成分生物合成提供了基因资源。

Objective To analyze the genome size and characteristics of the Chuanxiong(Ligusticum chuanxiong Hort.)by using flow cytometry and high-throughput sequencing technology,which provides a basis for the detailed sequencing of L.chuanxiong genome and the study of molecular mechanisms.Methods The genome size of L.chuanxiong was estimated by flow cytometry to use Lüdou[Vigna radiata(Linn.)Wilczek.]and Ludimian(Gossypium hirsutum L.)with known genome size as internal standard plants.High-throughput sequencing technology was used to conduct survey analysis of the L.chuanxiong genome.Then,bioinformatics was used to analyze the genome size,repeat sequence,heterozygosity,GC content,gene prediction,annotation and gene family identification and other information of L.chuanxiong.Results The genome size of L.chuanxiong was estimated to be about 3058.37 Mb,the repeat sequence,heterozygosity rate and GC content were respectively about 79.79%,2.16%,and 36.32%.It showed that the genome of L.chuanxiong was characterized by high repeatability,high heterozygosity and large genome.A total of 34864 genes were predicted,and 30737 genes were annotated in the functional database,and 53 genes were annotated in ferulic acid synthesis.A total of 2058 specific gene families and 2001 single-copy gene were identified.Conclusion The genome size,genome characteristics,functional genes and gene families of L.chuanxiong were initially obtained,which provides a reference for further whole-genome sequencing of L.chuanxiong,and also provide some gene resources for elucidating the biosynthesis of ferulic acid and other medicinal components in L.chuanxiong.