茜草叶绿体全基因组序列及其系统发育分析

以茜草科(Rubiaceae)植物茜草(Rubia cordifolia L.)为研究对象，采用Illumination高通量测序技术对其叶绿体全基因组进行测序，并运用MAGA11等生信学工具进行全基因组解析及系统发育分析。结果表明，(1)茜草叶绿体基因组呈典型的四分环状结构，总GC含量37.2%,长153 959 bp,其中包含大单拷贝(LSC)区83 844 bp、小单拷贝(SSC)区17 083 bp和2个反向重复(IR)区26 516 bp;共注释得到124个基因，包括79个蛋白质编码基因、37个tRNA和8个rRNA。(2)序列共鉴定到169个SSR位点，以A、T组成为主，包括129个单核苷酸、18个双核苷酸、11个三核苷酸、9个四核苷酸和2个五核苷酸，六核苷酸SSR未检测到；边界分析显示，茜草叶绿体基因组LSC区差异性最大，变异程度最高，而IRa区则差异性最小，最为保守。(3)最大似然法(ML)构建系统发育树显示，样品茜草与同属植物Rubia horrida以100%支持率聚为一类，茜草亚科、仙丹花亚科与金鸡纳亚科聚为姐妹类群，证明茜草科植物在进化过程中保守发育。

Complete Chloroplast Genome and Phylogenetic Analysis of Rubia cordifolia

Rubia cordifolia L., a plant in the Rubiaceae family. In this study, the whole chloroplast genome was sequenced by the high throughput sequencing technology of Illumination, and bioinformatics tools such as MAGA11 were used for genome analysis and phylogenetic analysis, so as to provide data reference for identification, genetic diversity analysis and resource exploitation and utilization of Rubia cordifolia and its related medicinal plants. The results showed that: (1) The chloroplast genome of Rubia cordifolia L. showed a typical quadripartite ring structure with a total GC content of 37.2%, a length of 153 959 bp, including a large single copy (LSC) region of 83 844 bp, a small single copy (SSC) region of 17 083 bp and two reverse repeat (IR) regions of 26 516 bp. A total of 124 genes were annotated, including 79 protein-coding genes, 37 tRNAs and 8 rRNAs. (2) A total of 169 SSRs were detected, mainly composed of A and T, including 129 mononucleotides, 18 dinucleotides, 11 trinucleotides, 9 tetranucleotides and 2 pentanucleotides, but no hexonucleotides were detected by SSR. Boundary analysis showed that the LSC region of Rubia cordifolia chloroplast genome had the largest difference and the highest degree of variation, while the IRa region had the smallest difference and was the most conservative. (3) The maximum likelihood method (ML) was used to construct phylogenetic tree, and the tree shows that Rubia cordifolia was grouped with the same species Rubia horrida with 100% support. The Rubioideae, Ixoroideae, and Cinchonoideae form the sister group, demonstrating that Rubiaceae has developed conserved during evolution. The results can provide data reference for identification, genetic diversity analysis and resource exploitation of Rubia cordifolia and its related species.