Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China
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...
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MDPI AG
2023-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/5/1083 |
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| author | Jing Chen Kaibing Zhou Xinwen Hu |
| author_facet | Jing Chen Kaibing Zhou Xinwen Hu |
| author_sort | Jing Chen |
| collection | DOAJ |
| description | 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 <i>Camellia gigantocarpa</i>, 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 <i>Camellia</i> genus did not belong to the same subclades. Meanwhile, the genetic relationship between the samples of <i>Camellia vietnamensis</i> and the undetermined species from Hainan Province or the population of <i>C. gauchowensis</i> in Xuwen was closer than that between <i>C. vietnamensis</i> and the population of <i>C. gauchowensis</i> in Luchuan, and the genetic relationship among <i>C. osmantha</i>, <i>C. vietnamensis</i> and <i>C. gauchowensis</i> 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. |
| first_indexed | 2024-03-11T03:42:55Z |
| format | Article |
| id | doaj.art-afabe28b970c4368a8e1949494a9a4cd |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T03:42:55Z |
| publishDate | 2023-05-01 |
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| spelling | doaj.art-afabe28b970c4368a8e1949494a9a4cd2023-11-18T01:30:15ZengMDPI AGGenes2073-44252023-05-01145108310.3390/genes14051083Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South ChinaJing Chen0Kaibing Zhou1Xinwen Hu2Sanya Nanfan Research Institute of Hainan University, Sanya 572025, ChinaSanya Nanfan Research Institute of Hainan University, Sanya 572025, ChinaSchool of Life Science, Hainan University, Haikou 570228, ChinaThe 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 <i>Camellia gigantocarpa</i>, 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 <i>Camellia</i> genus did not belong to the same subclades. Meanwhile, the genetic relationship between the samples of <i>Camellia vietnamensis</i> and the undetermined species from Hainan Province or the population of <i>C. gauchowensis</i> in Xuwen was closer than that between <i>C. vietnamensis</i> and the population of <i>C. gauchowensis</i> in Luchuan, and the genetic relationship among <i>C. osmantha</i>, <i>C. vietnamensis</i> and <i>C. gauchowensis</i> 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.https://www.mdpi.com/2073-4425/14/5/1083oil-tea camelliacpDNASNPsInDelsphylogenetic tree |
| spellingShingle | Jing Chen Kaibing Zhou Xinwen Hu Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China Genes oil-tea camellia cpDNA SNPs InDels phylogenetic tree |
| title | Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China |
| title_full | Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China |
| title_fullStr | Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China |
| title_full_unstemmed | Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China |
| title_short | Comparisons of Chloroplast Genome Mutations among 13 Samples of Oil-Tea Camellia from South China |
| title_sort | comparisons of chloroplast genome mutations among 13 samples of oil tea camellia from south china |
| topic | oil-tea camellia cpDNA SNPs InDels phylogenetic tree |
| url | https://www.mdpi.com/2073-4425/14/5/1083 |
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