作 者：
丁淑金;魏健生;陆莹玲;马福仙;原晓龙;耿云芬;王毅;张汉尧
单 位：
云南省林业科学院云南省森林植物培育与开发利用重点实验室;西南林业大学林学院
关键词：
油麦吊云杉;叶绿体基因组;密码子偏好性;最优密码子
摘 要：
[目的]分析油麦吊云杉cpDNA的特征和密码子偏好性,为云杉属植物叶绿体基因组学提供研究依据.[方法]通过Ilumina HiSeq测序平台对油麦吊云杉cpDNA进行测序,并利用Codon W 1.4.2 和CUSP软件对其密码子偏性进行分析.[结果]油麦吊云杉cpDNA是一个全长为 124161 bp的环状DNA分子,与典型的具有保守的四分体cpDNA结构不同,油麦吊云杉cpDNA中存在反向重复区域的丢失,其cpDNA的GC含量为38.7%.油麦吊云杉cpDNA包含 113 个基因,其中蛋白质编码基因 76 个,核糖体RNA基因 4 个,转运RNA基因 33 个,系统发育分析显示,油麦吊云杉和西加云杉聚为一个独特的分支,油麦吊云杉cpDNA密码子不同位置上的GC含量从低到高依次是GC3(49.39%)45 的占 86%,表明其密码子的偏性较弱;GC12 和GC3 的相关性不显著(r=0.1664,b=-0.1577);ENC频数比值分布在-0.05~0.05 的基因频率占比 57%,说明油麦吊云杉叶绿体基因组CUB受选择影响的同时也受到其他因素影响;油麦吊云杉cpDNA中大部分基因分布在PR2平面图的右下方,即T>A、G>C,说明在油麦吊云杉绿体基因组密码子的偏好性受选择、突变等因素的影响.最终UCU、AAA、GGU、GCA、GUU、UGU、UCC、CAU、GCU、CGU、GAA和AUU等 12 个密码子被确定为油麦吊云杉绿体基因组的最优密码子.[结论]油麦吊云杉cpDNA密码子偏好使用A或U结尾的密码子,选择和突变是其CUB的主要影响因素.
译 名：
Characteristics and codon usage bias of Picea brachytyla var.complanata chloroplast genome
作 者：
DING Shujin;WEI Jiansheng;LU Yingling;MA Fuxian;YUAN Xiaolong;GENG Yunfen;WANG Yi;ZHANG Hanyao;College of Forestry, Southwest Forestry University;The Key Laboratory of Biodiversity Conservation of Southwest China, National Forestry and Grassland Administration, Southwest Forestry University;Yunnan Provincial Key Laboratory of Cultivation and Exploitation of Forest Plants, Yunnan Academy of Forestry;Conservation of Rare, Endangered & Endemic Forest Plants, Public Key Laboratory of National Forestry and Grassland Administration, Yunnan Academy of Forestry;Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau;
关键词：
Picea brachytyla var.complanate;;chloroplast genome;;codon bias;;optimal codons
摘 要：
【Objective】This study was designed to analyze the codon usage bias and characteristics of the Picea brachytyla var.complanata chloroplast genome to provide a theoretical basis for the research of P. brachytyla.【Method】The chloroplast genome of P. brachytyla was sequenced using the Illumina Hiseq platform. Using CodonW 1.4.2 and the online software CUSP, we performed analysis on the codons of the P. brachytyla chloroplast genes and explored the infiuencing factors for codon preference.【Result】The cpDNA was a circular DNA molecule with a total length of 124,161bp. Unlike the typical chloroplast genome with a conserved quadripartite structure, the chloroplast genome of P. brachytyla exhibited a loss of inverted repeat regions, and the GC content was 38.7%. The genome contained 113 genes, including 76 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes.Further phylogenomic analysis showed that P. brachytyla and P. sitchensis were clustered in a unique clade in the Picea genus. The GC content at different locations of the cpDNA codons of P. brachytyla from low to high was GC3(49.39%) < GC2(40.73%) < GC1(30.48%), indicating the last codon of the chloroplast genome favored A and U. 86% of the cpDNA coding genes had an ENC value above 45, indicating that the codon bias was weak. The correlation coefficient between GC12 and GC3 indicated no significant correlation(r=0.166 4, b=-0.157 7). The ratio of ENC frequency in the range of-0.05 to 0.05 was 57%, suggesting that the preference for the codon usage pattern of the chloroplast genome of P. brachytyla was mostly affected by selection and other factors. Most of the genes in the chloroplast genome of P. brachytyla were distributed in the lower part of the PR2 plan, namely, T > A and G > C, suggesting that the preference of the codon usage of the chloroplast genome of P. brachytyla was affected by selection and mutation factors. Finally, 12codons such as UCU, AAA, GGU, GCA, GUU, UGU, UCC, CAU, GCU, CGU, GAA and AUU were determined as the optimal codons for the chloroplast genome of P. brachytyla.【Conclusion】The codon of P. brachytyla cpDNA prefers to use codons ending in A or U,which is mainly affected by selection and mutation.
