State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
Biomolecules. 2022 Oct 13;12(10):1474. doi: 10.3390/biom12101474.
is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of . In this study, 12 chloroplast genome sequences from nine species were determined using Illumina sequencing technology via assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus , a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (~400 bp) located in - region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus .
是山茶科中最大的属。由于表型多样性、频繁的杂交和多倍体化，物种间的系统发育关系的理解仍然具有挑战性。比较叶绿体（cp）基因组为的系统发育分析提供了一个信息丰富的资源。在这项研究中，使用 Illumina 测序技术通过组装，从 9 个物种中确定了 12 个叶绿体基因组序列。cp 基因组大小范围为 156545-157021bp，组织为具有典型被子植物 cp 基因组的四分体区域。每个基因组以相同的顺序和方向含有 87 个蛋白编码、37 个转移 RNA 和 8 个核糖体 RNA 基因。在 12 个 cp 基因组中检测到长链和短链重复序列、SNP 和 InDels 的差异。结合该属其他 7 个物种的完整 cp 序列，共鉴定出 9 个基因间序列分歧热点和 14 个具有高序列多态性的蛋白编码基因。这些热点，特别是位于 - 区的 InDel（约 400bp），具有足够的潜力作为进一步系统发育分析和物种鉴定的条形码标记。主成分和系统发育分析表明，区域限制而不是功能限制强烈影响了本研究中 cp 基因组的序列进化。这些 cp 基因组可以促进新的分子标记的开发、准确的物种鉴定以及该属的系统基因组关系的研究。
