| 法螺线粒体全基因组密码子偏好性分析 |
| |
| 引用本文： | 任童童,喻达辉,翟子钦,谭传港,何积翠,尚东维,陈移波,白丽蓉.法螺线粒体全基因组密码子偏好性分析[J].南方农业学报,2022,53(5):1379-1387. |
| |
| 作者姓名： | 任童童 喻达辉 翟子钦 谭传港 何积翠 尚东维 陈移波 白丽蓉 |
| |
| 作者单位： | 1 北部湾大学/广西北部湾海洋生物多样性养护重点实验室, 广西钦州 535011;2 天津农垦渤海农业集团有限公司, 天津 301823;3 天津嘉禾田源观赏鱼养殖有限公司, 天津 300481 |
| |
| 基金项目： | 广西自然科学基金项目（2021GXNSFAA075008）；北部湾大学海洋科学广西一流学科建设专项（DRB002）；广西北部湾海洋生物多样性养护重点实验室重点培育项目（2021ZB02）；广西北部湾海洋生物多样性养护重点实验室重大科技专项（2022ZA01） |
| |
| 摘 要： | 【目的】分析法螺（Charonia tritonis）线粒体基因组密码子偏好性，探究基因突变和自然选择对密码子偏好性的影响，为法螺属动物类群的系统发育树构建及种质资源保护与遗传改良提供参考依据。【方法】以法螺线粒体全基因组序列为材料，选择以ATG为起始密码子的非重复且长度大于300 bp的11个CDS（Coding DNA sequence）序列，采用CodonW 1.4.2进行密码子偏好性分析，并根据相对使用度差值（△RSCU）>0.08且RSCU在高表达基因库中>1.00的标准筛选出最优密码子。【结果】法螺线粒体基因组密码子第1位GC含量（GC1）的波动范围在35.80%~53.10%，平均为43.54%；第2位GC含量（GC2）的波动范围在32.40%~43.40%，平均为36.11%；第3位GC含量（GC3）的波动范围在23.00%~30.60%，平均为27.79%，GC1和GC2明显高于GC3；同义密码子第3位的GC含量（GC3S）的波动范围在20.90%~29.60%，平均为26.23%，表明密码子第3位碱基以A/U（T）结尾为主；密码子适应指数（CAI）的波动范围为0.096~0.166，平均为0.137；密码子偏好性指数（CBI）的波动范围在-0.212~-0.086，平均为-0.133；最优密码子使用频率（FOP）的波动范围为0.246~0.339，平均为0.306；有效密码子数目ENC的波动范围在44.37~51.69，平均为47.84；总平均亲水性（GRAVY）的变化范围在0.4419~1.4727，平均为0.9501。中性绘图分析、ENC-plot绘图分析及对应性分析均表明，在法螺线粒体基因组密码子偏好性的形成过程中受基因突变和自然选择的双重作用，但以自然选择为主导。综合高表达优越密码子和高频密码子，最终确定出11个密码子为法螺线粒体基因组最优密码子，分别为UUU、CUA、GUA、UAU、CAA、AAA、UCA、CCA、ACA、GCC和GCA，其中有1个密码子以G/C结尾，其余10个密码子均以A/U结尾。【结论】法螺线粒体基因组密码子偏好以A/U（T）结尾，筛选确定的11个最优密码子主要以A/U结尾。法螺线粒体基因组密码子为弱偏好性密码子，自然选择在其偏好性的形成过程中起主导作用。
|
| 关 键 词： | 法螺 线粒体基因组 密码子偏好性 最优密码子 自然选择 |
| 收稿时间： | 2022-03-23 |
Analysis of codon usage bias in mitochondrial genome of Charonia tritonis |
| |
| REN Tong-tong,YU Da-hui,ZHAI Zi-qin,TAN Chuan-gang,HE Ji-cui,SHANG Dong-wei,CHEN Yi-bo,BAI Li-rong.Analysis of codon usage bias in mitochondrial genome of Charonia tritonis[J].Journal of Southern Agriculture,2022,53(5):1379-1387. |
| |
| Authors: | REN Tong-tong YU Da-hui ZHAI Zi-qin TAN Chuan-gang HE Ji-cui SHANG Dong-wei CHEN Yi-bo BAI Li-rong |
| |
| Affiliation: | 1 Beibu Gulf University/Guangxi Key Laboratory of Guangxi Beibu Gulf Marine Biodiversity Conservation, Qinzhou, Guangxi 535011, China;2 Tianjin Nongken Bohai Agricultural Group Co., Ltd., Tianjin 301823, China;3 Tianyuan Jiahe Ornamental Fish Breeding Co., Ltd., Tianjin 300481, China |
| |
| Abstract: | 【Objective】To analyze codon usage bias of the mitochondrial genome of Charonia tritonis and to explore effects of gene mutation and natural selection on codon usage bias，so as to provide reference for phylogenetic tree construction，germplasm resources protection and genetic improvement of C. tritonis.【Method】Mitochondrial genome of C. tritonis was taken as material and 11 CDSs（Coding DNA sequences）from the whole genome sequence of C. tritonis mitocondria were screened out，which were non-repeated sequences more than 300 bp and started from ATG，by using the software of CodonW 1.4.2 for codon usage bias analysis and optimal codons were selected with △RSCU>0.08 and RSCU> 1.00 in highly expressed gene bank.【Result】GC content in position 1（GC1）ranged from 35.80% to 53.10% with an average of 43.54%. GC content in position 2（GC2）ranged from 32.40% to 43.40% with an average of 36.11%. GC content in position 3（GC3）ranged from 23.00% to 30.60% with an average of 27.79%. GC1 and GC2 contents were obviously higher than GC3 content. GC content in position 3 of synonymous codon（GC3s）ranged from 20.90% to 29.60% with an average of 26.23%，suggesting that codon third-base mainly ended with A/U（T）. Codon adaptation index（CAI）ranged from 0.096 to 0.166 with an average of 0.137. Codon bias index（CBI）ranged from -0.212 to -0.086 with an average of -0.133. Frequency of optimal codons（FOP）ranged from 0.246 to 0.339 with an average of 0.306. Effective number of codon（ENC）ranged from 44.37 to 51.69 with an average of 47.84. Grand average of hydropathicity（GRAVY）ranged from 0.4419 to 1.4727 with an average of 0.9501. Neutrality plots，ENC-plot and correspondence analysis results showed that the codon bias of mitochondrial genome in C. tritonis was affected by both gene mutation and natural selection but dominantly by the latter. Finally，considering high frequency codons and high expression codons，11 codons were identified as the optimal codons in the mitochondrial genome of C. tritonis，and they were UUU，CUA，GUA，UAU，CAA， AAA，UCA，CCA，ACA，GCC and GCA，among which one ended with G/C，and the rest 10 ended with A/U.【Conclusion】The results show that the codons prefer to end with A/U（T）base，and the 11 screened optimal codons prefer to end with A/U base in mitochondrial genome of C. tritonis. In mitochondrial genome of C. tritonis，the codons show weak bias，natural selection play a leading role in the formation of codon usage bias. |
| |
| Keywords: | |
|
| 点击此处可从《南方农业学报》浏览原始摘要信息 |
|
点击此处可从《南方农业学报》下载全文 |
|
