南五味子属叶绿体基因组密码子偏好性分析  

Analysis of Codon Usage Bias in the Chloroplast Genome of Kadsura

作　　者：刘涛[1] 尹登攀 金吉芬 彭志军[1] 李兴忠[1] 汪得凯 LIU Tao;YIN Deng-pan;JIN Ji-fen;PENG Zhi-jun;LI Xin-zhong;WANG De-kai(Citrus Fruit Research Institute in Guizhou Province,Guiyang 550027,Guizhou,China;College of Life Sciences and Medicine,Zhejiang Sci-Tech University,Hangzhou 310018,Zhejiang,China;Institute of Crop Germplasm Resources,Guizhou Academy of Agricultural Sciences,Guiyang 550027,Guizhou,China)

机构地区：[1]贵州省果树科学研究所,贵州贵阳550027 [2]浙江理工大学生命科学与医药学院,浙江杭州310018 [3]贵州省农作物品种资源研究所,贵州贵阳550027

出　　处：《西北林学院学报》2023年第5期102-109,共8页Journal of Northwest Forestry University

基　　金：贵州省科技平台项目(黔科合服企〔2021〕8号);浙江理工大学科研启动基金(19042142-Y)。

摘　　要：为探究南五味子属植物叶绿体基因组密码子的使用偏好性及影响因素,利用Codon W 1.4.2、CUSP及EMBOSS等程序,进行中性绘图、ENC-plot及PR2-plot绘图分析。结果表明,南五味子属4个物种的叶绿体基因组密码子总体偏性较弱,只有rps14的ENC值小于40;物种间的密码子参数高度保守,GC_(2)对ENC影响较大;有31个密码子RSCU大于1,均以A/U结尾;自然选择在4个物种叶绿体基因组同义密码子使用偏性中发挥主导作用;南五味子属4个物种中分别确定了18、17、16和18个最优密码子,共有的最优密码子有14个;在ΔR_(SCU)>0.5的高频密码子中,仅有编码半胱氨酸(Cys)的UGU为共有最优密码子。表明南五味子属4个物种间密码子偏好性较保守,自然选择是影响密码子偏好性的主要因素。研究结果为南五味子属物种鉴定、保护和遗传改良提供了基础。To investigate the codon preference and affecting factors of the chloroplast genome of medicinal plants in the Kadsura genus,neutral mapping,ENC plot,and PR2 plot analysis were conducted by using programs such as Codon W 1.4.2,CUSP,and EMBOSS.The results indicated that the overall codon bias was weak,except that the ENC value of rps14(33.00±0.26)was less than 40.The chloroplast genome codon parameters were highly conserved in the four Kadsura species and GC_(2) had a greater impact on ENC.There were 31 codons with a relative synonymous codon usage(RSCU)greater than 1 and preferred to end with A/U,indicating that it is more biased towards the use of codons ending with A/U in the four species of Kadsura.It was found that natural selection played a dominant role in the synonymous codon usage bias of chloroplast genomes of four Kadsura species.Totally,18,17,16 and 18 optimal codons were identified from four Kadsura species,respectively,and there were 14 optimal codons in common.Among the high-frequency codons withΔR_(SCU)>0.5,only UGU encoding cysteine(Cys)was the consensus optimal codon,indicating that the high-frequency optimal codon usage differed significantly among four species.In summary,the codon bias of chloroplast genomes in four species of Kadsura is weak,and the codon bias among species is relatively conservative.Natural selection is the main factor affecting the codon bias.

关 键 词：南五味子属 叶绿体基因组 偏好性 最优密码子 

分 类 号：S796[农业科学—林木遗传育种]