婆婆纳叶绿体基因组测序与特征分析

Sequencing and Characterization of Chloroplast Genome of Veronica polita

摘要

婆婆纳(Veronica polita Fr.)是一种重要的藏药材, 本研究基于高通量测序方法完成了婆婆纳叶绿体基因组的测序, 并运用生物信息学方法分析了其结构、基因构成等特征, 随后利用叶绿体基因组的蛋白质编码序列探讨了婆婆纳的系统发育关系。结果表明: 1) 婆婆纳的完整叶绿体基因组总长为150 191 bp, GC含量为37.9%, 具有典型的四分体环状结构, 大单拷贝(large single copy, LSC)区、小单拷贝(small single copy, SSC)区和反向重复(inverted repeat, IR)区的长度分别为81 847 bp、17 414 bp和25 456 bp; 2) 婆婆纳叶绿体基因组含有134个基因, 包括88个蛋白质编码基因(protein coding gene, PCG)、8个核糖体RNA (ribosomal RNA, rRNA)基因、38个转运RNA (transfer RNA, tRNA)基因, 其中假基因2个; 3) 在婆婆纳叶绿体基因组中共检测到26 529个密码子, 其中32种密码子的相对同义密码子使用度(relative synonymous codon usage, RSCU)值小于1, 30种密码子的RSCU值大于1, 2种密码子的RSCU值等于1; 4) 婆婆纳属植物的IR边界高度保守, 无明显的收缩或扩张; 5) 婆婆纳属植物叶绿体基因组之间的变异区域多在基因间隔区; 6) 婆婆纳与阿拉伯婆婆纳(V. persica)的亲缘关系较近。本研究为婆婆纳属物种的鉴定和遗传多样性研究提供了基础资料。

Abstract

Veronica polita Fr. is an important Tibetan medicinal herb. Herein, the chloroplast genome of V. polita was sequenced based on high-throughput sequencing, and its basic characteristics were analyzed using bioinformatics methods. The phylogeny of V. polita was studied using the protein coding sequences of chlo-roplast genomes. The results were as follows: 1) The complete chloroplast genome of V. polita is 150 191 bp in length, with a GC content of 37.9%. The lengths of large single copy (LSC), small single copy (SSC) and inverted repeat (IR) regions are 81 847 bp, 17 414 bp and 25 456 bp, respectively; 2) The chloroplast genome contains 134 genes, including 88 protein coding genes (PCGs), 8 ribosomal RNA (rRNA) genes and 38 trans-port RNA (tRNA) genes, including 2 pseudogenes; 3) A total of 26 529 codons were detected in the chloro-plast genome. Among them, 32 types of single codons have relative synonymous codon usage (RSCU) values less than 1, 30 types have RSCU values greater than 1, and 2 types have RSCU values equal to 1; 4) The IR boundary regions of Veronica are highly conservative, without obvious contraction or expansion; 5) Most varia-tions in chloroplast genomes of Veronica plants exist in intergenic regions; 6) V. polita is most closely related to V. persica. This study laid the foundation for species identification and genetic diversity research of the genus Veronica.

关键词

婆婆纳 / 藏药 / 叶绿体基因组 / 测序 / 特征

Key words

Veronica polita / Tibetan medicine / chloroplast genome / sequencing / characterization