摘要
【目的】探讨方格星虫线粒体基因组密码子偏好性,明确自然选择和基因突变对其密码子偏好性的作用,并充分利用密码子偏好性的特点,为方格星虫分子遗传改良提供科学依据。【方法】根据方格星虫线粒体基因组序列,选取长度大于300 bp且以ATG开头的10个非重复基因序列为研究对象,运用CondonW 1.4.2分析方格星虫线粒体基因组密码子偏好性参数,通过中性绘图分析、ENC-plot分析、PR2-plot分析及对应分析明确方格星虫线粒体基因组密码子偏好性形成的主导因素,并依据高频密码子和高表达密码子筛选出方格星虫线粒体基因组最优密码子。【结果】方格星虫线粒体基因组密码子的GC含量因位置而异,GC1、GC2和GC3的平均值分别为51.06%、40.19%和47.11%,GC含量平均值为46.12%;ENC、CAI和CBI的平均值依次为50.022、0.150和-0.023;RSCU>1.00的同义密码子有31个,以A或C结尾的密码子占87.10%。中性绘图分析结果表明,GC12与GC3无相关性,相关系数为0.05;ENC-plot分析结果表明,全部参试基因均位于标准曲线下方,说明方格星虫线粒体基因组密码子偏好性以自然选择为主导;PR2-plot分析结果表明,除ND6基因位于左侧x轴上外,其余9个参试基因全部分布在坐标系的第二象限;对应分析结果表明,前4轴的贡献率分别为23.86%、14.96%、12.21%和10.82%,在构建的平面坐标系内细胞色素C类基因分布相对集中,而NADH还原酶类基因分布较分散。依据方格星虫线粒体基因组的高频密码子和高表达密码子,最终确定GUA、CUC、CAC、CUU、AUU、CCU、GCA、AAC及GAA为方格星虫线粒体基因组最优密码子。【结论】方格星虫线粒体基因组密码子偏好性较弱,偏好于A/C结尾的密码子;自然选择在方格星虫线粒体基因组密码子偏好性形成中占主导地位。因此,可根据宿主线粒体基因组密码子偏好性优化外源基因,以提高其表达效率,加速方格星虫品种的遗传改良。
【Objective】To explore the codon bias of the mitochondrial genome in Sipunculus nudus for the effects of natural selection and genetic mutation on the codon bias,and make full use of the characteristics of the bias to provide scien-tific basis for the molecular genetic improvement of S.nudus.【Method】According to the mitochondrial genome sequence of S.nudus,ten non-repetitive gene sequences with more than 300 bp in length and starting with ATG were selected as research objects.CondonW 1.4.2 was used to analyze the codon bias parameters of the mitochondrial genome in S.nudus.Neutral plot analysis,ENC-plot analysis,PR2-plot analysis and corresponding analysis were applied to reveal the domi-nant factors in the formation of codon bias of the mitochondrial genome,and optimal codons in the mitochondrial genome were determined based on high-frequency and high-expression codons.【Result】The GC content of the mitochondrial gene codons varied with the position.The averages of GC1,GC2 and GC3 were 51.06%,40.19%and 47.11%respectively.The average GC content was 46.12%;the averagesof ENC,CAI,and CBI were 50.022,0.150 and-0.023 respectively;there were 31 synonymous codons of RSCU>1.00 with codons ending with A or C accounting for 87.10%.The neutral plot analysis showed that there was no correlation between GC12 and GC3,with the correlation coefficient being 0.05;the ENC-plot analysis indicated that all tested genes were located below the standard curve,suggesting that the codon bias of the mitochondrial genome was shaped by natural selection;the PR2-plot analysis showed that nine genes were scat-tered in the second quadrant of the coordinate system,except ND6 gene on the left x-axis;the corresponding analysis showed that the contribution rates of the first four axes were 23.86%,14.96%,12.21%and 10.82%respectively.In the co-ordinate system,the distribution of cytochrome C genes was relatively concentrated,while the distribution of NADH re-ductase genes was relatively scattered.Based on the high-frequency and high-expression codons in the mitochondrial ge-nome,nine codons including GUA,CUC,CAC,CUU,AUU,CCU,GCA,AAC and GAA were finally determined to be the optimal codons in the mitochondrial genome in S.nudus.【Conclusion】The codon bias of the mitochondrial gene of S.nudus is weak,preferring codons ending in A/C;natural selection plays a dominant role in shaping the codon bias of the mitochondrial genome in S.nudus.Therefore,exogenous genes can be optimized on the basis of the codons bias of mi-tochondrial gene in the host to improve their expression efficiency and accelerate the genetic improvement of varieties of S.nudus.
作者
韩春丽
杨果豪
李天香
王健宇
熊忠萍
许尤厚
朱鹏
杨家林
王鹏良
HAN Chun-li;YANG Guo-hao;LI Tian-xiang;WANG Jian-yu;XIONG Zhong-ping;XU You-hou;ZHU Peng;YANG Jia-lin;WANG Peng-liang(College of Marine Science,Beibu Gulf University,Qinzhou,Guangxi 535011,China)
出处
《南方农业学报》
CAS
CSCD
北大核心
2023年第9期2604-2613,共10页
Journal of Southern Agriculture
基金
广西重点研发计划项目(桂科AB21220061)
广西科技重大专项(桂科AA19254008-3)。
