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<p>The tea tree resources in Shaoyang exhibit significant diversity, particularly with wild tea tree Germplasms. This work chose 30 full chloroplast genomes for comparative genomics and phylogenetic analysis to elucidate the genesis and evolutionary relationships of these tea tree resources. The selection comprised 8 freshly sequenced genomes from Shaoyang tea plants and 22 species genomes sourced from the NCBI GenBank collection. The research demonstrated that the chloroplast genomes of Shaoyang tea plants possess a unique quadripartite configuration, with sizes varying from 156,697 to 157,098&#xa0;bp. The structure comprises a large single-copy region (LSC, 86,236–86,642&#xa0;bp), a minor single-copy section (SSC, 18,268–18,292&#xa0;bp), and a pair of inverted repeat sequences (IRs, 26,025–26,090&#xa0;bp). The genomes comprise 132–134 functional genes, encompassing 87–89 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. The Shaoyang tea tree genome's structure, gene content, simple sequence repeats (SSRs), and long repeat sequences (LSRs) were analyzed comparatively, demonstrating that these characteristics are conserved across various tea tree genomes. Sequence difference analysis revealed that genes such as <i>rpoC2</i>, <i>ndhA</i>, <i>ycf1</i> and <i>ycf2</i> may have undergone positive selection. This study also identified 11 highly variable regions, including three intergenic regions (<i>trnG-UCC</i>, <i>trnT-GGU</i>, and <i>trnL-CAA-ndhB</i>) and eight gene regions (<i>atpF</i>, <i>accD</i>, <i>petD</i>, <i>rps8</i>, <i>rps19</i>, <i>ndhD</i>, <i>rps15</i>, and <i>ycf1</i>). The phylogenetic analysis results reveal a distinct differentiation within the Shaoyang tea plants population, categorizing it into two separate clades: <i>C. shunhuangshanwildtea</i>1 and <i>C. shunhuangshanwildtea</i>2 cluster with <i>C. duntsa</i>, <i>C. anhua</i>, and <i>C. fudingdabaicha</i> in one clade; <i>C. guidingcha</i>1, <i>C. tingpingdong</i>, and <i>C. gulonggrouptea</i>1 cluster with <i>C. shunhuangshanwildtea</i>3 and <i>C. shunhuangshanwildtea</i>4 in another clade. This study systematically analyzed the resources of Shaoyang tea plants, revealing their rich genetic diversity and unique evolutionary features, providing scientific basis and genomic resources for germplasm resource identification, diversity development, breeding and genetic improvement.</p>

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Comparative chloroplast genomic analysis: uncovering variations and phylogenetic relationships in tea plants from Shaoyang, Hunan Province, China

  • 期刊论文

  • 发表日期：

    2025年8月21日

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  • Jin Li,
  • Yu Qin,
  • Jun Tang,
  • Xiao-Yan Qiu,
  • Chang-Qing Xie,
  • Han Tang,
  • Ai-Ming Tang,
  • Xiao Chen,
  • Jun-Ping Xie,
  • Hua Luo

摘要

The tea tree resources in Shaoyang exhibit significant diversity, particularly with wild tea tree Germplasms. This work chose 30 full chloroplast genomes for comparative genomics and phylogenetic analysis to elucidate the genesis and evolutionary relationships of these tea tree resources. The selection comprised 8 freshly sequenced genomes from Shaoyang tea plants and 22 species genomes sourced from the NCBI GenBank collection. The research demonstrated that the chloroplast genomes of Shaoyang tea plants possess a unique quadripartite configuration, with sizes varying from 156,697 to 157,098 bp. The structure comprises a large single-copy region (LSC, 86,236–86,642 bp), a minor single-copy section (SSC, 18,268–18,292 bp), and a pair of inverted repeat sequences (IRs, 26,025–26,090 bp). The genomes comprise 132–134 functional genes, encompassing 87–89 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. The Shaoyang tea tree genome's structure, gene content, simple sequence repeats (SSRs), and long repeat sequences (LSRs) were analyzed comparatively, demonstrating that these characteristics are conserved across various tea tree genomes. Sequence difference analysis revealed that genes such as rpoC2, ndhA, ycf1 and ycf2 may have undergone positive selection. This study also identified 11 highly variable regions, including three intergenic regions (trnG-UCC, trnT-GGU, and trnL-CAA-ndhB) and eight gene regions (atpF, accD, petD, rps8, rps19, ndhD, rps15, and ycf1). The phylogenetic analysis results reveal a distinct differentiation within the Shaoyang tea plants population, categorizing it into two separate clades: C. shunhuangshanwildtea1 and C. shunhuangshanwildtea2 cluster with C. duntsa, C. anhua, and C. fudingdabaicha in one clade; C. guidingcha1, C. tingpingdong, and C. gulonggrouptea1 cluster with C. shunhuangshanwildtea3 and C. shunhuangshanwildtea4 in another clade. This study systematically analyzed the resources of Shaoyang tea plants, revealing their rich genetic diversity and unique evolutionary features, providing scientific basis and genomic resources for germplasm resource identification, diversity development, breeding and genetic improvement.