刺果甘草全基因组Survey及叶绿体基因组特征分析＊

目的 基于基因组Survey分析对刺果甘草Glycyrrhiza pallidiflora Maxim.基因组大小和杂合率进行估计,并通过叶绿体基因组序列特征对其在甘草属Glycyrrhiza L.中的系统发育位置进行研究。方法 使用二代测序技术对刺果甘草进行测序,采用K-mer方法对测序reads进行分析,估算刺果甘草基因组大小和杂合率,使用生物信息学方法进行叶绿体基因组组装、注释和系统发育分析。结果 Survey分析结果显示其基因组大小约为577.82 Mb,杂合度约为0.31%,重复序列比例约为53.72%。叶绿体基因组长度为127,267 bp,不具有典型的四分体结构,总GC含量为34.32%,包含110个基因,其中76个蛋白质编码基因,30个tRNA基因和4个rRNA基因。系统发育分析表明,刺果甘草与圆果甘草G. squamulosa Franch.亲缘较接近。结论 刺果甘草存在低杂合和重复序列较多的特点,为了更好地对全基因组进行序列拼接和组装,可尝试采用三代测序结合二代测序的分析策略进行基因组组装;刺果甘草叶绿体全基因组比对和系统发育分析,为后续开展甘草属遗传多样性研究和分子鉴定标记筛选提供了重要依据。

Genome Survey and Chloroplast Genome Analysis of Glycyrrhiza pallidiflora Maxim

Objectives To estimate genome size and heterozygosity, and study the phylogeny of G. pallidiflora by chloroplast genome sequence characteristics, based on genome Survey analysis of Glycyrrhiza pallidiflora Maxima.Methods The genome of G. pallidiflora was sequenced by second-generation sequencing technology. The K-mer method was used to analyze the sequenced reads to estimate the genomic size and heterozygosity of G. pallidiflora; chloroplast genome assembly, annotation, and phylogenetic analysis were conducted by using the bioinformatics method.Results The genome Survey of G. pallidiflora showed that its genome size was about 577.82 Mb and its heterozygosity was 0.31%, and the proportion of repetitive sequences was approximately 53.72%. The chloroplast genome was 127,267 bp in length without a typical tetrad structure, and the total GC content was 34.32%. The chloroplast genome contained 110 genes, of which 76 were protein-coding genes, 30 were tRNA genes, and 4 were rRNA genes. Phylogenetic analysis based on chloroplast genome sequence showed that G. pallidiflora was the closest to G. squamulosa.Conclusion G. pallidiflora is characterized by low heterozygosity and a large number of repeated sequences. In order to better splice and assemble the whole genome, the analysis strategy of third-generation sequencing combined with second-generation sequencing should be used to assemble the genome. Phylogenetic analysis and genome-wide alignment analysis of G. pallidiflora have provided an essential basis for further genetic diversity and molecular marker screening of G. species.