罗氏沼虾转录组密码子使用偏好性分析  

Analysis of Codon Usage Bias Based on Macrobrachium rosenbergii Transcriptome

作　　者：慎佩晶[1] 张宇飞[1] 李喜莲[1] 高强[1] 徐洋[1] 黄振远[1] 蒋文枰[1] 陈雪峰[1] SHEN Pei-jing;ZHANG Yu-fei;LI Xi-lian;GAO Qiang;XU Yang;HUANG Zhen-yuan;JIANG Wen-ping;CHEN Xue-feng(Genetics and Breeding Research Laboratory,Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture,Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang province,Zhejiang Institute of Freshwater Fisheries,Huzhou Zhejiang 313001)

机构地区：[1]遗传育种研究室/农业农村部淡水渔业健康养殖重点实验室/浙江省淡水水产遗传育种重点实验室/浙江省淡水水产研究所,浙江湖州313001

出　　处：《现代农业科技》2020年第16期175-178,184,共5页Modern Agricultural Science and Technology

基　　金：国家重点研发计划“蓝色粮仓科技创新”专项(2018YFD0901303);浙江省农业(水产)新品种选育重大科技专项(2016C02055-2)。

摘　　要：以罗氏沼虾转录组数据为数据来源,通过研究罗氏沼虾转录组的密码子使用参数(如有效密码子的数量和相关密码子碱基的具体组成信息等),并且采用Codon W 1.4.4深入开展了统计和计算.研究结果显示,同义密码子第三位核苷酸和表达基因密码子GC含量均值分别为0.40和0.45.从整体上看,ENC的平均值等于52.72,其中绝大部分的ENC值小于35.采用高频密码子的研究方法获得GAU、GAA、UUU、AAU、CCA等5个高频密码子.通过最优码子分析法确定16个最优密码子,编码10个氨基酸,最优密码子除UUG外均以A/T结尾.而且把它和大肠杆菌、酵母、果蝇以及人类等6种生物的密码子使用频率开展比较,结果表明,与大肠杆菌和果蝇存在较大差异,而与酵母最为接近.研究结果可为罗氏沼虾功能基因和分子育种等提供理论基础.Using the transcriptome data of Macrobrachium rosenbergii as the data source,CodonW1.4.4 software was used to analyze and study the codon usage,and other codon usage parameters such as the transcript base composition and actual codon number of Macrobrachium rosenbergii,and the expression genes of Macrobrachium rosenbergii were found.The results showed that the average GC content of the codon was 0.45,and the average GC content of the third nucleotide of the synonym codon was 0.40.The mean ENC of the expressed gene was 52.72,and most of the ENC values were less than 35.Five high-frequency codons of GAU,GAA,UUU,AAU and CCA were determined by high-frequency codon analysis.Sixteen optimal codons were determined by optimal codon analysis and 10 amino acids were encoded.The optimal codons all ended in A/T except UUG.Comparing the codon usage frequency of Macrobrachium rosenbergii with six other species such as Escherichia coli,Saccharomyces cervisiae,Drosophila melanogaster,Homo sapiens,etc.,it was found to be quite different from Escherichia coli and Drosophila melanogaster,but it was almost consistent with Saccharomyces cerevisiae.The research provided a theoretical basis for functional genome research and molecular breeding of Macrobrachium rosenbergii.

关 键 词：罗氏沼虾 偏好性 转录组 密码子 

分 类 号：S968.12[农业科学—水产养殖]