Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships
文献类型： 外文期刊
作者： Chen, Zhiyin 1 ; Liu, Qing 1 ; Xiao, Ying 1 ; Zhou, Guihua 1 ; Yu, Penghui 2 ; Bai, Jing 1 ; Huang, Hua 3 ; Gong, Yihui 1 ;
作者机构： 1.Hunan Univ Humanities Sci & Technol, Coll Agr & Biotechnol, Loudi 417000, Peoples R China
2.Hunan Acad Agr Sci, Tea Res Inst, Changsha 410125, Peoples R China
3.Guangdong Acad Agr Sci, Inst Fruit Tree Res, Key Lab South Subtrop Fruit Biol & Genet Resource, Guangdong Prov Key Lab Trop & Subtrop Fruit Tree R, Guangzhou 510640, Peoples R China
关键词： Camellia sinensis L; cv; 'Zhuyeqi'; Chloroplast genome; Assembly; SSR loci; Phylogeny
期刊名称：JOURNAL OF APPLIED GENETICS （ 影响因子：2.4； 五年影响因子：3.0 ）
ISSN： 1234-1983
年卷期： 2023 年
页码：
收录情况： SCI
摘要： The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.
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