Guan Bicai, Wen Jianteng, Guo Hanjing, Liu Yizhen
College of Life Sciences, Nanchang University, Nanchang, China.
Front Plant Sci. 2024 Mar 13;15:1306196. doi: 10.3389/fpls.2024.1306196. eCollection 2024.
This study presents a comprehensive analysis of the chloroplast (cp) genomes of species, including comparative and phylogenetic evaluations, as well as examinations of their genomic structure and composition. The cp genomes exhibit a typical circular quadripartite structure and demonstrate highly similar gene order and genomic structure. The complete cp genome size of the 10 taxa in this study is 156,965 bp to 157,383 bp, where the length of the large single-copy (LSC) region is 86,296 bp to 86,691 bp, small single-copy (SSC) region is 18,386 bp to 18,454 bp, and inverted repeat (IR) region is 23,143 bp to 26,112 bp. A total of 131 genes were found, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. The mean GC content of the 10 taxa is 38.145%, where the LSC region is 36.396%, the SSC region is 32.372%, and the IR region is 43.076%. Despite the relatively conserved nature of the cp genome within the species of , 25-31 simple sequence repeats (SSRs) were identified in the 10 taxa in our study. The SSRs were found to be distributed in the LSC, SSC, and IR regions in subsp. , subsp. , subsp. , and subsp. , while the SSR was not found in the IR region of the other six taxa. Thus, whole cp genomics is a valuable tool for species identification, taxonomic clarification, and genomic evolutionary analysis. Furthermore, our findings reveal that and subsp. , along with and , form sister groups. Notably, subsp. and subsp. did not exhibit affinity with subsp. . Our study furnishes essential data for further research on their classification and provides novel insights into the relationship within subg. .
本研究对[物种名称]的叶绿体（cp）基因组进行了全面分析，包括比较和系统发育评估，以及对其基因组结构和组成的研究。cp基因组呈现典型的环状四分体结构，基因顺序和基因组结构高度相似。本研究中10个分类单元的完整cp基因组大小为156,965 bp至157,383 bp，其中大单拷贝（LSC）区域长度为86,296 bp至86,691 bp，小单拷贝（SSC）区域为18,386 bp至18,454 bp，反向重复（IR）区域为23,143 bp至26,112 bp。共发现131个基因，包括86个蛋白质编码基因（PCG）、8个rRNA基因和37个tRNA基因。10个分类单元的平均GC含量为38.145%，其中LSC区域为36.396%，SSC区域为32.372%，IR区域为43.076%。尽管cp基因组在[物种名称]物种内相对保守，但在我们的研究中，10个分类单元中鉴定出了25 - 31个简单序列重复（SSR）。在[亚种名称1]、[亚种名称2]、[亚种名称3]和[亚种名称4]的LSC、SSC和IR区域发现了SSR，而在其他六个分类单元的IR区域未发现SSR。因此，全cp基因组学是物种鉴定、分类学澄清和基因组进化分析的宝贵工具。此外，我们的研究结果表明，[物种名称1]和[亚种名称1]，以及[物种名称2]和[物种名称3]形成姐妹群。值得注意的是，[亚种名称2]和[亚种名称3]与[亚种名称1]没有亲缘关系。我们的研究为进一步研究它们的分类提供了重要数据，并为[亚属名称]内的关系提供了新的见解。
