摘要
为揭示山铜材(Chunia bucklandioides)叶绿体基因组基本结构和蛋白编码信息,以及为未来研究山铜材的分子标记、基因工程和遗传多样性等提供参考,基于高通量测序数据对山铜材的叶绿体基因组全序列进行组装和分析。结果表明,山铜材叶绿体基因组总长度为159801 bp,呈典型的四分体结构,基因组的GC含量为38.1%,有效密码子数(ENC)为35.19~54.38,含131个编码基因,其中有80个蛋白编码基因,8个rRNA和37个tRNA,并鉴定出71个简单重复序列位点;根据中性绘图、有效密码子数绘图、偏倚性绘图分析表明,山铜材叶绿体基因组的蛋白编码基因在密码子选择过程中主要受自然选择的影响,更倾向于使用A、U碱基进行编码;相对密码子使用度>1的高频密码子有29个,其中有28个以A或U结尾,筛选出的8个最优密码子分别为GCU、GAU、GGA、AAU、CCU、AGA、UCA、ACA。山铜材叶绿体基因组的组装和分析揭示了其四分体结构、基因组成及密码子使用偏好性,明确了自然选择在密码子选择中的主导作用,并显示出对A、U结尾密码子的高度偏好。
The study aimed to reveal the basic structure and protein coding information of the chloroplast genome of Chunia bucklandioides,with the aim of providing a reference for future research on its molecular markers,genetic engineering,and genetic diversity.Based on high-throughput sequencing data,the complete chloroplast genome sequence of C.bucklandioides was assembled and analyzed.The total length of the genome was 159801 bp,with a typical tetrad structure.The GC content of the genome was 38.1%,and the number of effective codons(ENC)was 35.19-54.38.The genome contained 131 coding genes,including 80 protein-coding genes,8 rRNAs,and 37 tRNAs.In addition,71 simple repeated sequence loci were identified.Neutral,ENC,and PR2 plots revealed that the protein-coding genes of the chloroplast genome of C.bucklandioides were mainly influenced by natural selection during codon selection,and tended to use A and U bases for encoding.There were 29 high-frequency codons with relative synonymous codon usage>1,of which 28 ended at A or U.GCU,GAU,GGA,AAU,CCU,AGA,UCA,and ACA were selected as the optimal codons.Assembly and analysis of the chloroplast genome of C.bucklandioides revealed its tetrad structure,gene composition,and codon usage preference;clarified the dominant role of natural selection in codon selection;and showed a high preference for A and U end codons.
作者
王晨璐
黄振北
赖文峰
施国政
刘浩洋
张国防
WANG Chenlu;HUANG Zhenbei;LAI Wenfeng;SHI Guozheng;LIU Haoyang;ZHANG Guofang(College of Forestry,Fujian Agriculture and Forestry University,Fuzhou,Fujian 350002,China;Fujian Minhou Baisha State Owned Forest Farm,Fuzhou,Fujian 350102,China;Research Institute of Tropical Forestry,Chinese Academy of Forestry,Guangzhou,Guangdong 510520,China)
出处
《森林与环境学报》
北大核心
2025年第1期82-90,共9页
Journal of Forest and Environment
基金
福建省林木种苗技术攻关项目(K42MLI05A)
林学学科《珍贵经济树种种质与高效培育》创新团队支持计划项目。
