虎杖叶绿体基因组结构与变异分析

Genome structure and variation of Reynoutria japonica Houtt. chloroplast genome

摘要:

虎杖（Reynoutria japonica Houtt.）为蓼科（Polygonaceae）蓼族（Polygoneae）虎杖属（Reynoutria Houtt.）植物，是一种传统的中草药，具有利湿退黄、清热解毒、散瘀止痛、止咳化痰的功效。本研究采取高通量测序技术获得5个虎杖品种的叶绿体全基因组序列，并与NCBI已公布的蓼族何首乌（Fallopia multiflora）和金线草（Antenoron filiforme）等植物的叶绿体全基因组序列进行了基因组学和系统发育分析。通过基因组学分析发现，5种虎杖的叶绿体基因组大小有163 376 bp和163 371 bp两种情况，并呈现出典型的环状四分体结构，85 784 bp的一条较长的单拷贝区（large single-copy region，LSC），18 616 bp的一条较短的单拷贝区（small single-copy region，SSC），还有两条长度一致的反向重复区，分别为IRa区和IRb区相间隔分布。通过注释得到161个基因，其中蛋白编码基因106个，rRNA编码基因10个，tRNA编码基因45个。总GC含量为36.7%，其中LSC、SSC和IR区域的GC含量分别为34.8%、30.7%和42.7%。对比不同虎杖品种叶绿体的全基因组分析发现，trnk-UUU、rpoC1、petD、rpl16、ndhA、rpl12基因的编码区发生了变异。系统发育分析显示，虎杖5个品种聚为一枝，处在已知11种蓼族材料最原始的位置，与何首乌构成姐妹群。

关键词:中草药;叶绿体全基因组;基因组学分析;环状四分体

Abstract:

Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).

Key words:Chinese medicinal herb;whole chloroplast genome;genomics analysis;circular tetrad structure