College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, Hunan, China.
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
BMC Genomics. 2022 Sep 8;23(1):639. doi: 10.1186/s12864-022-08872-3.
Sinosenecio B. Nordenstam (Asteraceae) currently comprises 44 species. To investigate the interspecific relationship, several chloroplast markers, including ndhC-trnV, rpl32-trnL, matK, and rbcL, are used to analyze the phylogeny of Sinosenecio. However, the chloroplast genomes of this genus have not been thoroughly investigated. We sequenced and assembled the Sinosenecio albonervius chloroplast genome for the first time. A detailed comparative analysis was performed in this study using the previously reported chloroplast genomes of three Sinosenecio species.
The results showed that the chloroplast genomes of four Sinosenecio species exhibit a typical quadripartite structure. There are equal numbers of total genes, protein-coding genes and RNA genes among the annotated genomes. Per genome, 49-56 simple sequence repeats and 99 repeat sequences were identified. Thirty codons were identified as RSCU values greater than 1 in the chloroplast genome of S. albonervius based on 54 protein-coding genes, indicating that they showed biased usage. Among 18 protein-coding genes, 46 potential RNA editing sites were discovered. By comparing these chloroplast genomes' structures, inverted repeat regions and coding regions were more conserved than single-copy and non-coding regions. The junctions among inverted repeat and single-copy regions showed slight difference. Several hot spots of genomic divergence were detected, which can be used as new DNA barcodes for species identification. Phylogenetic analysis of the whole chloroplast genome showed that the four Sinosenecio species have close interspecific relationships.
The complete chloroplast genome of Sinosenecio albonervius was revealed in this study, which included a comparison of Sinosenecio chloroplast genome structure, variation, and phylogenetic analysis for related species. These will help future research on Sinosenecio taxonomy, identification, origin, and evolution to some extent.
山莴苣属（ Asteraceae ）目前包含 44 个物种。为了研究种间关系，人们使用了几个叶绿体标记，包括 ndhC-trnV、rpl32-trnL、matK 和 rbcL，来分析山莴苣属的系统发育。然而，该属的叶绿体基因组尚未得到彻底研究。本研究首次对山莴苣属山莴苣的叶绿体基因组进行了测序和组装，并对先前报道的三种山莴苣属叶绿体基因组进行了详细的比较分析。
结果表明，四种山莴苣属植物的叶绿体基因组均呈现典型的四分体结构。注释基因组中总基因、蛋白编码基因和 RNA 基因的数量相等。每个基因组中鉴定出 49-56 个简单序列重复和 99 个重复序列。基于 54 个蛋白编码基因，在山莴苣属山莴苣的叶绿体基因组中鉴定出 30 个密码子的 RSCU 值大于 1，表明它们存在偏好性使用。在 18 个蛋白编码基因中，发现了 46 个潜在的 RNA 编辑位点。通过比较这些叶绿体基因组的结构，发现反转重复区和编码区比单拷贝区和非编码区更保守。反转重复区和单拷贝区之间的连接处存在微小差异。检测到几个基因组分化热点，可作为物种鉴定的新 DNA 条形码。整个叶绿体基因组的系统发育分析表明，四种山莴苣属植物具有密切的种间关系。
本研究揭示了山莴苣属山莴苣的完整叶绿体基因组，包括山莴苣属叶绿体基因组结构、变异和相关种系发生分析的比较。这些将在一定程度上有助于山莴苣属的分类学、鉴定、起源和进化的未来研究。
