森林茶园古茶树大理茶叶绿体基因组密码子偏好性及系统发育研究

佟岩; 黄荟; 王雨华

doi:10.13305/j.cnki.jts.2023.03.010

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茶叶科学 ›› 2023, Vol. 43 ›› Issue (3) : 297-309. DOI: 10.13305/j.cnki.jts.2023.03.010

研究报告

森林茶园古茶树大理茶叶绿体基因组密码子偏好性及系统发育研究

佟岩¹, 黄荟^1,2, 王雨华^1,*

作者信息 +

Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden

TONG Yan¹, HUANG Hui^1,2, WANG Yuhua^1,*

Author information +

文章历史 +

摘要

大理茶（Camellia taliensis）是古茶林森林茶园的重要茶种之一,参与了大叶茶的起源驯化。为了解大理茶叶绿体基因组密码子偏好性,探讨影响密码子偏好性形成的因素,对其进行了中性绘图分析、ENC-plot、PR2-plot分析,并寻找最优密码子。结果表明,大理茶叶绿体54条编码序列（CDS）的GC含量为37.68%,GC₁、GC₂的含量分别为46.44%、39.77%,高于GC₃（27.67%）,说明其叶绿体基因组密码子末位碱基偏好以A、U结尾;有效密码子数ENC范围为35.64~56.67,平均值为46.1,表明其密码子偏好性较弱;中性绘图分析、ENC-plot分析和PR2-plot偏倚分析表明,影响大理茶叶绿体密码子偏好性的主要因素是自然选择;有11个密码子被确定为最优密码子。虽然基于matK基因和CDS序列构建的茶组植物系统发育树显示的拓扑结构有所不同,但所有树型均显示大理茶与秃房茶聚为一支,且是栽培茶的近缘种。本研究为解析大理茶的遗传进化,系统发育提供了基础,为大理茶重要农艺性状改良提供了科学依据。

Abstract

Camellia taliensis is one of the important tea plants which is often grown in forest-tea gardens, which participated in the origin and domestication of C. sinensis var. assamica. To determine the codon usage bias pattern and its main influencing factors in the chloroplast genome of C. taliensis, neutral plotting, ENC-plot, PR2-plot analyses were performed and the optimal codons were found. The results show that the GC content of 54 CDS sequences was 37.68%, while GC₁ and GC₂ content were 46.44% and 39.77%, higher than GC₃(27.67%), indicating that the third base of the codon preferred to end in A/U. The effective codon number (ENC) ranged from 35.64 to 56.67 , with an average value of 46.1, demonstrating weak codon usage bias in chloroplast genome of C. taliensis. Neutral plotting, ENC-plot, PR2-plot analyses show that the main factor affecting the codon usage bias of the C. taliensis chloroplast genome was natural selection. In total, 11 optimal codons were identified in the chloroplast genome of C. taliensis. Although phylogenetic trees constructed by matK gene and CDS sequence display different topological structures, all trees show that C. taliensis and C. gymnogyna are clustered into one branch and are closely related to cultivated tea plant. This study provided the basis for analyses of genetic evolution, phylogeny and improved agronomic traits of C. taliensis.

导出引用

佟岩, 黄荟, 王雨华. 森林茶园古茶树大理茶叶绿体基因组密码子偏好性及系统发育研究[J]. 茶叶科学. 2023, 43(3): 297-309 https://doi.org/10.13305/j.cnki.jts.2023.03.010

TONG Yan, HUANG Hui, WANG Yuhua. Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden[J]. Journal of Tea Science. 2023, 43(3): 297-309 https://doi.org/10.13305/j.cnki.jts.2023.03.010

中图分类号： S571.1

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