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泰国四种本土物种的完整叶绿体基因组:结构、比较和系统发育分析。

Complete Chloroplast Genome of Four Thai Native Species: Structural, Comparative and Phylogenetic Analyses.

机构信息

Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.

Faculty of Law, Khon Kaen University, Khon Kaen 40002, Thailand.

出版信息

Genes (Basel). 2023 Mar 12;14(3):703. doi: 10.3390/genes14030703.

Abstract

The chloroplast genomes of , . , . , and . are 153,370-153,503 bp in size. A total of 113 genes were predicted, including 79 protein-coding sequences (CDS), 30 tRNA, and four rRNA genes. The overall GC content for all four species was 37%. Only mono-, di-, and trinucleotides were present in the genome. Genes adjacent to the junction borders were similar in all species analyzed. Eight distinct indel variations were detected in the chloroplast genome alignment of 24 species. At a cut-off point of Pi = 0.03, a sliding window analysis based on 25 chloroplast genome sequences of species revealed three highly variable regions, which included three CDS (C, 1, and 32), as well as an intergenic spacer region, F-32. A phylogenetic tree based on the complete chloroplast genome sequence displayed an almost fully resolved relationship in . However, , , and were clustered together with while was closely related to . As is a diverse genus, genome data generated in this study may contribute to a better understanding of the genetic identity of these species, which would be useful for future taxonomic work of .

摘要

,.,., 和. 的叶绿体基因组大小为 153,370-153,503bp。共预测到 113 个基因,包括 79 个蛋白编码序列(CDS)、30 个 tRNA 和 4 个 rRNA 基因。四个物种的总 GC 含量均为 37%。基因组中仅存在单核苷酸、二核苷酸和三核苷酸。分析的所有物种中,基因与交界边界相邻。在对 24 种 叶绿体基因组序列的比对中检测到 8 个独特的插入缺失变异。在基于 25 个 叶绿体基因组序列的 Pi = 0.03 截断点的滑动窗口分析中,发现了三个高度可变区域,其中包括三个 CDS(C、1 和 32)以及一个内含子间隔区 F-32。基于完整叶绿体基因组序列构建的系统发育树显示, 中的关系几乎完全得到解决。然而, 、 、 和 与 聚在一起,而 与 关系密切。由于 是一个多样化的属,本研究产生的基因组数据可能有助于更好地了解这些物种的遗传同一性,这对未来的 分类工作将是有用的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06dd/10048501/0a22d173cab6/genes-14-00703-g001.jpg

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