白芷全基因组测序分析及BGLU基因家族分析

Complete genome sequencing and BGLU gene family analysis of Angelica dahurica

关键词:  杭白芷, 基因组, 第三代测序技术, BGLU基因家族, 药用植物

Key words:  Angelica dahurica var. formosana, genome, the third-generation sequencing technology, BGLU gene family, medicinal plant

摘要:

白芷为常用的药食同源物种,既是临床常用中药,又是香料,用途十分广泛。为获取白芷全基因组序列信息,该研究首次以杭白芷叶片DNA为材料,采用 Nanopore 测序技术构建杭白芷全基因组数据库,并利用生物信息学方法对获得的核苷酸序列进行组装、功能注释以及进化分析研究。结果表明:(1)原始测序数据过滤后获得662 Gb三代数据,Read N50约为32 932 bp,经过组装得到杭白芷基因组大小为5.6 Gb,Contig N50 约为806 638 bp。(2)组装后的序列通过与 KOG、GO、KEGG 等功能数据库比对,得到了功能注释的基因占66.47%,KOG功能注释结果表明杭白芷的蛋白功能主要集中在一般功能预测、翻译后修饰、蛋白质转换、伴侣以及信号转导机制; GO功能分类表明杭白芷的基因集中在生物学过程及细胞组分; KEGG通路注释表明参与代谢途径的基因占主要地位。(3)杭白芷中鉴定到45个BGLU家族基因。该研究首次利用第三代测序技术对杭白芷全基因组进行解析,为杭白芷的系统生物学研究和BGLU在杭白芷生长发育中的后续功能研究提供了重要的理论参考。

Abstract:

Angelica dahurica is a common species of medicine and food homology, which is not only a common clinical traditional Chinese medicine, but also a spice, with a wide range of uses. In order to obtain the whole genome sequence information of A. dahurica, we used A. dahurica var. formosana leaf DNA as material, and the Nanopore sequencing technology was used to establish its nucleotide sequences database, then genome assembly, function annotation and evolution analysis were carried out by bioinformatic methods. The results were as follows:(1)A total of 662 Gb of the third-generation data were obtained after fittering the original sequencing data, with the Read N50 about 32 932 bp. The assembled A. dahurica genome size was 5.6 Gb, Contig N50 was about 806 638 bp.(2)The genes were with gene annotations accounted for 66.47% after being compared with functional databases such as NR, KOG and KEGG. The result of KOG gene annotation was that the protein function of A. dahurica concentrated in the general functional prediction, posttranslational modification, protein turnover, chaperones and signal transduction mechanisms. GO functional classification indicated that the genes of A. dahurica concentrated on cell biological processes and components. KEGG analysis found that the A. dahurica genes mostly involved in metabolic pathways.(3)And 45 genes of BGLU family were identified in A. dahurica. In this study, the whole genome of A. dahurica is resolved by the third-generation sequencing technology for the first time, which provides important theoretical references for the systematic biological study and the further study of the function of BGLU in the growth and development of A. dahurica.