Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China.
School of Life Science, Hainan University, Haikou 570228, China.
Genes (Basel). 2023 May 14;14(5):1083. doi: 10.3390/genes14051083.
The differences in cpDNA SNPs and InDels of 13 samples from single trees of different species or populations of oil-tea camellia in South China were examined in this study, and phylogenetic trees were reconstructed based on CDSs and non-CDSs of cpDNAs to research the evolutionary relationships among all samples. The SNPs of all samples included all kinds of substitutions, and the frequency of the transition from AT to GC was highest; meanwhile, the frequencies of all kinds of transversions differed among the samples, and the SNPs exhibited polymorphism. The SNPs were distributed in all the different functional regions of cpDNAs, and approximately half of all SNPs in exons led to missense mutations and the gain or loss of termination codons. There were no InDels in the exons of any cpDNA samples, except those retrieved from , although this InDel did not lead to a frame shift. The InDels of all cpDNA samples were unevenly distributed in the intergenic region and upstream and downstream of genes. The genes, regions of the same gene, sites and mutation types in the same region related to the distributions of SNPs, and InDels were inconsistent among samples. The 13 samples were divided into 2 clades and 7 or 6 subclades, and the samples of species from the same sections of the genus did not belong to the same subclades. Meanwhile, the genetic relationship between the samples of and the undetermined species from Hainan Province or the population of in Xuwen was closer than that between and the population of in Luchuan, and the genetic relationship among , and was very close. In sum, SNPs and InDels in the different cpDNAs resulted in variable phenotypes among the different species or populations, and they could be developed into molecular markers for studies on species and population identification and phylogenetic relationships. The conclusion from the identification of undetermined species from Hainan Province and the phylogenetic relationships among 13 oil-tea camellia samples based on cpCDS and cpnon-CDS sequences were the same as those from the former report.
本研究检测了华南地区不同种或种群的油茶单株 13 个样本的 cpDNA SNPs 和 InDels，基于 cpDNA 的 CDS 和非 CDS 重建了系统发育树，以研究所有样本间的进化关系。所有样本的 SNPs 包括各种取代，且 AT 到 GC 的转换频率最高；同时，各种颠换在样本间的频率不同，且 SNPs 表现出多态性。SNP 分布于 cpDNA 的所有不同功能区，外显子中的大约一半 SNPs 导致错义突变和终止密码子的获得或丢失。除了从海南和徐闻采集的样本外，所有 cpDNA 样本的外显子中均没有 InDels，尽管这些 InDel 没有导致移码。所有 cpDNA 样本的 InDels 不均匀分布于基因间区及上下游。基因、同一基因的区域、同一区域的位点和突变类型的分布与 SNPs 和 InDels 相关，在样本间不一致。13 个样本分为 2 个分支和 7 或 6 个亚分支，来自同一属的不同种的样本未归属于同一亚分支。同时，来自海南或徐闻的未确定种与 的样本间的遗传关系比来自鹿川的 与 的样本间的遗传关系更近，且 、 与 的遗传关系非常近。总之，不同 cpDNA 中的 SNPs 和 InDels 导致不同种或种群间表型的变化，它们可以作为物种和种群鉴定及系统发育关系研究的分子标记。基于 cpCDS 和 cpnon-CDS 序列对海南未确定种的鉴定和 13 个油茶样本的系统发育关系的结论与之前的报道相同。
