Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, China.
Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai 317000, China.
Genes (Basel). 2024 Feb 20;15(3):263. doi: 10.3390/genes15030263.
is a species of the Lauraceae family, which has important medicinal, economic and ornamental values. In this study, we sequenced, assembled and annotated the chloroplast genome of and reannotated and corrected eight unverified annotations in the same genus. The chloroplast genomes taxa from Lindera and from different genera of Lauraceae were compared and analyzed, and their phylogenetic relationship and divergence time were speculated. All the 36 chloroplast genomes had typical quadripartite structures that ranged from 150,749 to 154,736 bp in total length. These genomes encoded 111-112 unique genes, including 78-79 protein-coding genes, 29-30 tRNA and 4 rRNA. Furthermore, there were 78-97 SSRs loci in these genomes, in which mononucleotide repeats were the most abundant; there were 24-49 interspersed repeats, and forward repeat types were the most frequent. The codon bias patterns of all species tended to use codons ending with A or U. Five and six highly variable regions were identified within genus and between genera, respectively, and three common regions (, and ) were identified, which can be used as important DNA markers for phylogeny and species identification. According to the evaluation of the Ka/Ks ratio, most of the genes were under purifying selection, and only 10 genes were under positive selection. Finally, through the construction of the evolutionary tree of 39 chloroplast genomes, the phylogenetic relationship of Lauraceae was clarified and the evolutionary relationship of was revealed. The species of genus experienced rapid adaptive radiation from Miocene to Pleistocene. The results provided valuable insights for the study of chloroplast genomes in the Lauraceae family, especially in the genus .
是樟科植物的一个种，具有重要的药用、经济和观赏价值。本研究对其叶绿体基因组进行了测序、组装和注释，并对同一属的 8 个未经证实的注释进行了重新注释和修正。比较和分析了来自樟科不同属的 36 个叶绿体基因组，推测了它们的系统发育关系和分化时间。所有 36 个叶绿体基因组都具有典型的四分体结构，总长为 150749-154736bp。这些基因组共编码 111-112 个特有基因，包括 78-79 个蛋白编码基因、29-30 个 tRNA 和 4 个 rRNA。此外，这些基因组中有 78-97 个 SSR 位点，其中单核苷酸重复最为丰富；有 24-49 个散布重复，正向重复类型最为频繁。所有物种的密码子偏性模式都倾向于使用以 A 或 U 结尾的密码子。在属内和属间分别鉴定出 5 个和 6 个高度可变区，同时鉴定出 3 个共有区（、和 ），可作为系统发育和物种鉴定的重要 DNA 标记。根据 Ka/Ks 比值的评估，大多数基因受到纯化选择，只有 10 个基因受到正选择。最后，通过构建 39 个叶绿体基因组的进化树，阐明了樟科的系统发育关系，并揭示了 的进化关系。属 中的物种在中新世到更新世经历了快速的适应性辐射。这些结果为樟科植物叶绿体基因组的研究，特别是属 的研究提供了有价值的见解。
