| 瓜螺线粒体全基因组密码子偏好性分析 |
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| 引用本文： | 何积翠,喻达辉,白丽蓉.瓜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(1):191-199. |
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| 作者姓名： | 何积翠 喻达辉 白丽蓉 |
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| 作者单位： | 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 |
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| 基金项目： | 广西自然科学基金;广西重点研发计划项目;国家重点研发计划 |
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| 摘 要： | 【目的】探究瓜螺（Melo melo）线粒体全基因组密码子使用偏好性，明确影响密码子偏好性的因素，为提高基因表达效率及了解瓜螺线粒体基因组的特性和进化方向提供科学依据。【方法】以瓜螺线粒体全基因组序列为研究对象，从中筛选出11条长度大于300 bp且以ATG为起始密码子的非重复基因序列，利用CodonW 1.4.2、Excel 2017及SPSS 22.0等软件进行瓜螺线粒体全基因组密码子偏好性分析。【结果】不同基因序列密码子位置所对应的G+C含量不同，其中，GC1（密码子第1位所代表的G+C含量）、GC2（密码子第2位所代表的G+C含量）、GC3（密码子第3位所代表的G+C含量）的变化范围分别为35.20%~51.90%、16.40%~40.60%和13.10%~34.90%，对应平均值为41.15%、32.29%和23.71%，GC1和GC2明显高于GC3；密码子适应指数（CAI）在0.110~0.180，平均为0.137；密码子偏好性指数（CBI）在-0.272~-0.090，平均为-0.175；最优密码子使用频率（FOP）在0.216~0.339，平均为0.277；有效密码子数（ENC）在36.84~53.75，平均为45.59；总平均亲水性（GRAVY）在0.480~1.394，平均为0.968。有30个同义密码子的相对使用度（RSCU）大于1.00，且主要以A/U结尾。中性绘图分析发现，GC1和GC2平均值（GC12）与GC3的相关系数为-0.438，相关性不显著（P>0.05，下同）；ENC-plot绘图分析结果显示，各散点（基因）均位于标准曲线附近，其中，NAD4、COX2和NAD3基因位于标准曲线上方，COX1、ATP6、NAD1、NAD6、COB、NAD5、COX3及NAD2等8个基因位于标准曲线下方；在对应性分析中，第一、第二、第三、第四向量轴的贡献率分别23.12%、15.19%、13.17%和9.63%，前4轴累计差异为61.12%。综合高频密码子与高表达密码子，最终筛选出4个最优密码子（UUU、GUU、ACU和CAU），且均以U结尾。【结论】瓜螺线粒体全基因组密码子偏好以A/U结尾的形式，筛选出的4个最优密码子（UUU、GUU、ACU和CAU）均以U结尾。除了自然选择在瓜螺线粒体全基因组密码子偏好性形成中占主导地位外，突变压力和碱基组成也影响其密码子偏好。因此，可通过瓜螺目的基因密码子优化，有效提高外源基因表达且优化性状决定基因，从而加速瓜螺优良亲本培育的进程。
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| 关 键 词： | 瓜螺 线粒体 基因组 密码子偏好性 自然选择 |
| 收稿时间： | 2021-08-30 |
Codon usage bias analysis in mitochondrial genome of Melo melo |
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| HE Ji-cui,YU Da-hui,BAI Li-rong.Codon usage bias analysis in mitochondrial genome of Melo melo[J].Journal of Southern Agriculture,2022,53(1):191-199. |
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| Authors: | HE Ji-cui YU Da-hui BAI Li-rong |
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| Institution: | Beibu Gulf University/Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, Guangxi 535011, China |
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| Abstract: | 【Objective】The use preference of mitochondrial whole genome codon of Melo melo was investigated，and the factors affecting codon preference were analyzed，to improve gene expression efficiency，study the characteristics， ecological adaptation and evolutionary direction of mitochondrial genome of M. melo.【Method】Based on the mitochondrial genome sequence of M. melo，eleven non-repetitive sequences with length more than 300 bp and ATG as the starting codon were selected as the research objects，and the codon bias was analyzed by using the softwares of CodonW 1.4.2， Excel 2017，SPSS 22.0.【Result】The G+C content corresponding to codon positions of different gene sequence varies，including GC（1 G+C content represented by codon position 1），GC（2 G+C content represented by codon position 2），GC3 （G+C content represented by codon position 3），was 35.20%-51.90%，16.40%-40.60%，13.10%-34.90%，corresponding average of 41.15%，32.29%，and 23.71%，respectively. The content of GC1 and GC2 was higher than that of GC3. The codon adaptation index（CAI ）value ranged from 0.110 to 0.180，with an average of 0.137. The codonbiasindex（CBI） was at -0.272 to -0.090，with an average of -0.175. The optimal codon usage frequency（FOP）was from 0.216-0.339， with an average of 0.277. The effective codon number（ENC）ranged from 36.84 to 53.75，with an average of 45.59； grand average of hydropathy（GRAVY）ranged from 0.480 to 1.394，with an average of 0.968. There were 30 codons with relative synonymous codon usage（RSCU）>1.00，mainly ending with A/U. Neutral mapping analysis showed that the correlation coefficient between the mean of GC1 and GC（2 GC12）and GC3 was -0.438，the correlation was not significant（P>0.05，the same below）. ENC-plot analysis showed that all genes were located near the standard curve，among them，NAD4，COX2 and NAD3 genes were located above the standard curve，and eight genes including COX1，ATP6， NAD1，NAD6，COB，NAD5，COX3 and NAD2 were located below the standard curve. Correspondence analysis showed that the first，second，third and fourth axis contributed 23.12%，15.19%，13.17% and 9.63% of the difference，respectively. The total contribution rate of the first four vectors was 61.12%. Combining high frequency codons and high expression codons，four optimal codons（UUU，GUU，ACU and CAU）were selected，all ending with U.【Conclusion】The whole mitochondrial genome codon of M. melo mainly prefers to use the codon ending in A/U，and the four selected optimal codons（UUU，GUU，ACU，and CAU）end with U. In addition to dominating natural selection in genome-wide codon preference formation in M. melo mitochondria，mutational pressure and base composition also influence their codon preference. Codon optimization of the target gene can effectively improve the foreign gene expression and optimize the trait determination gene，so as to accelerate the process of excellent parental cultivation. |
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