Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution.
Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution.
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家蚕线粒体基因组密码子使用偏向性分析及其与进化的关系
DOI：
10.1186/s12862-014-0262-4
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发表时间：
2014-12-17
影响因子：
3.4
通讯作者：
Sun J
中科院分区：
文献类型：
--
作者：
Wei L;He J;Jia X;Qi Q;Liang Z;Zheng H;Ping Y;Liu S;Sun J
同义密码子使用偏性（Synonymous codon usage bias，SCUB）是生物分类中不可避免的现象，通常指不同物种或同一物种基因组内密码子出现频率的差异。SCUB在自然选择、突变偏好等因素的压力下，以不同的方式发生。对家蚕基因表达和物种进化也有重要意义，但对家蚕（B.森）尚未报道。此外，关于造成这种偏差的原因以及这种偏差与B进化之间的关系，目前还不清楚。结果比较了B的基因组DNA（gDNA）和线粒体DNA（mtDNA）的密码子使用模式。mori认为mtDNA具有更高水平的密码子偏好性。对应分析表明，基因长度、基因功能和翻译选择等自然选择对mtDNA的密码子偏好性起主导作用，而突变偏好性的组成限制仅起次要作用。此外，家蚕超家族的聚类结果表明，丝裂基因组密码子使用与物种进化之间的关系缺乏明确性。结论在导致密码子偏好性的复杂影响因素中，自然选择在形成B mtDNA的高偏好性中起主要作用。从我们目前的数据来看。虽然聚类分析表明密码子偏好性与物种进化关系不大，但对有丝分裂基因组密码子使用的详细分析可以更好地了解鳞翅目昆虫的进化关系。然而，mtDNA的偏好性与进化之间的关系还需要更多新的方法和数据来研究。
BackgroundSynonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the same species. SCUB happens in various degrees under pressure from nature selection, mutation bias and other factors in different ways. It also attaches great significance to gene expression and species evolution, however, a systematic investigation towards the codon usage in Bombyx mori (B. mori) has not been reported yet. Moreover, it is still indistinct about the reasons contributing to the bias or the relationship between the bias and the evolution of B. mori.ResultsThe comparison of the codon usage pattern between the genomic DNA (gDNA) and the mitochondrial DNA (mtDNA) from B. mori suggests that mtDNA has a higher level of codon bias. Furthermore, the correspondence analysis suggests that natural selection, such as gene length, gene function and translational selection, dominates the codon preference of mtDNA, while the composition constraints for mutation bias only plays a minor role. Additionally, the clustering results of the silkworm superfamily suggest a lack of explicitness in the relationship between the codon usage of mitogenome and species evolution.ConclusionsAmong the complicated influence factors leading to codon bias, natural selection is found to play a major role in shaping the high bias in the mtDNA of B. mori from our current data. Although the cluster analysis reveals that codon bias correlates little with the species evolution, furthermore, a detailed analysis of codon usage of mitogenome provides better insight into the evolutionary relationships in Lepidoptera. However, more new methods and data are needed to investigate the relationship between the mtDNA bias and evolution.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
DOI：
10.1073/pnas.96.8.4482
发表时间：
1999-04-13
影响因子：
11.1
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Mouchiroud, D
DOI：
10.1016/j.bbrc.2014.06.087
发表时间：
2014-07-25
影响因子：
3.1
作者：
Ihara, Hideyuki;Okada, Takahiro;Ikeda, Yoshitaka
通讯作者：
Ikeda, Yoshitaka
影响因子：
3.5
作者：
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影响因子：
2.9
作者：
Burton, R. S.;Ellison, C. K.;Harrison, J. S.
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