高山植物唐古红景天叶绿体基因组特征及系统发育分析

Characteristics of chloroplast genome and phylogenetic analysis of alpine plant Rhodiola tangutica (Crassulaceae)

关键词:  红景天属，唐古红景天，叶绿体基因组，系统发育，密码子偏好性

Key words:  Rhodiola, Rhodiola tangutica, Chloroplast genome, Phylogeny, Codon preference

摘要:

为了明确西北地区重要药用植物唐古红景天（Rhodiola tangutica）的叶绿体基因组结构特点、基因信息和系统发育关系，该研究利用Illumina NovaSeq6000对基因组进行了测序，运用GeSeq、PGA、NOVOPlasty、IRscope、MISA等多种生物信息学分析软件对其结构、基因功能和亲缘关系进行分析。结果表明：（1）唐古红景天的叶绿体基因组呈四分体环状结构，由82 121 bp LSC、16 996 bp SSC和25 873 bp IR区构成，全长150 863 bp，总GC含量为37.8%，IR区GC含量最高（42.9%）；编码131个基因，包括85个PCGs、38个tRNAs和8个rRNAs。（2）检测到32 471个密码子，其中编码半胱氨酸（Cys）最少（1.18%）、异亮氨酸（Ile）密码子占比最多（8.24%），29种密码子的RSCU值均大于1。（3）IR区分析显示，rps19和ndhF均向IRB扩张。（4）系统发育分析表明，唐古红景天与四裂红景天（Rhodiola quadrifida）的亲缘最近，分歧时间估计显示红景天属Rhodiola物种的起源时间平均为15.50 Mya（95% HPD：6.0-21.0 Mya）。该研究明晰了唐古红景天的叶绿体基因组特征，获得了红景天属物种较为合理的系统发育关系，为红景天属遗传多样性研究、适应性进化机制讨论以及种质资源保护等提供了理论依据。

Abstract:

In order to explore the structure characteristics, gene information and phylogenetic relationship of the chloroplast genome for Rhodiola tangutica, which is an important medicinal plant growing in Northwest China, this study sequenced its complete chloroplast genome using the high-throughput sequencing technology with Illumina NovaSeq6000. We analyzed the genome structure, gene function and genetic relationship of the chloroplast genome based on NOVOPlasty, GeSeq, PGA, IRscope and MISA. The results were as follows: (1) The chloroplast genome of R. tangutica had a typical and quadripartite circular structure of 150 863 bp in length, including LSC (82 121 bp), SSC (16 996 bp) and IR (25 873 bp). Total GC content was 37.8%, among which the IR regions had the highest (42.9%). The genome encoded 131 genes in total, including 85 PCGs, 38 tRNAs and eight rRNAs. (2) Among the 32 471 codons, cysteine (Cys) had the smallest percentage (1.18%), while isoleucine (Ile) had the highest (8.24%). There were 29 codons with the value of RSCU above one. (3) The analysis of IR regions showed that both rps19 and ndhF were expanded into the IRB region. (4) Phylogenetic analysis indicated that R. tangutica and R. quadrifida had the closest relationship. Estimates of divergence times indicated that the origin of Rhodiola species was estimated to be around 15.50 Mya (95% HPD: 6.0-21.0 Mya). In this study, we clarified the chloroplast genome characteristics of Rhodiola tangutica and obtained a reasonable phylogenetic relationship of Rhodiola, which provided a theoretical basis for the study of genetic diversity, the discussion of adaptive evolutionary mechanism and the protection of germplasm resources of Rhodiola.