Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution

文献类型： 外文期刊

第一作者： Wei, Lei

作者： Wei, Lei;Jia, Xian;Qi, Qi;Liang, Zhisheng;Zheng, Hao;Ping, Yao;Sun, Jingchen;He, Jian;Liu, Shuyu

作者机构：

关键词： Bombyx mori;Synonymous codon usage bias;Genomic DNA;Mitochondrial DNA;Evolution

期刊名称：BMC EVOLUTIONARY BIOLOGY （ 影响因子：3.26； 五年影响因子：3.732 ）

ISSN： 1471-2148

年卷期： 2014 年 14 卷

页码：

收录情况： SCI

摘要： Background: Synonymous 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. Results: The 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. Conclusions: Among 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.

分类号：

  • 相关文献

[1]Molecular phylogeny of the domesticated silkworm, Bombyx mori, based on the sequences of mitochondrial cytochrome b genes. Li, AL,Zhao, QL,Tang, SM,Zhang, ZF,Pan, SY,Shen, GF.

[2]Dicrocoelium chinensis and Dicrocoelium dendriticum (Trematoda: Digenea) are distinct lancet fluke species based on mitochondrial and nuclear ribosomal DNA sequences. Liu, Guo-Hua,Yan, Hong-Bin,Wang, Xing-Ye,Jia, Wan-Zhong,Zhu, Xing-Quan,Otranto, Domenico,Wang, Xing-Ye,Zhao, Guang-Hui.

[3]A novel approach obtaining intron-containing hairpin RNA constructs. Cai, Ping-Zhong,Wen, Chun-Miao,Xu, Zheng-Jun,Zhong, Wan-Fang.

[4]Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity. Qi, Yueying,Xu, Wenjing,Xing, Tian,Zhao, Mingming,Yan, Li,Xia, Guangmin,Wang, Mengcheng,Li, Nana. 2015

[5]Phenotypic and genotypic changes in rapeseed after 18 years of storage and regeneration. Wu, XM,Wu, NF,Qian, XZ,Li, RG,Huang, FH,Zhu, L. 1998

[6]Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. Kang, Houxiang,Yang, Yuhong,Zhang, Zhonghua,Zhang, Shengping,Mao, Zhenchuan,Cheng, Guohua,Gu, Xingfang,Huang, Sanwen,Xie, Bingyan,Weng, Yiqun,Kang, Houxiang,Yang, Yuhong,Zhang, Zhonghua,Zhang, Shengping,Mao, Zhenchuan,Cheng, Guohua,Gu, Xingfang,Huang, Sanwen,Xie, Bingyan.

[7]Cloning and SNP screening of the TLR4 gene and the association between its polymorphism and somatic cell score in dairy cattle. Xu, Shang-zhong,Gao, Xue,Li, Jun-ya,Ren, Hong-yan,Wang, Xing-ping,Luoren, Zhuo-ma.

[8]Trypanosoma (Herpetosoma) grosi: First isolation from Chinese striped field mouse (Apodemus agrarius). Guan, Guiquan,Niu, Qingli,Yang, Jifei,Li, Youquan,Gao, Jinliang,Luo, Jianxun,Yin, Hong.

[9]Development and characterization of 19 microsatellite markers for Collichthys lucidus. Ma, Chunyan,Ma, Hongyu,Ma, Lingbo,Cui, Haiyu,Ma, Qunqun,Cui, Haiyu,Ma, Qunqun.

[10]Functional analysis of GUS expression patterns and T-DNA integration characteristics in rice enhancer trap lines. Peng, H,Huang, HM,Yang, YZ,Zhai, Y,Wu, JX,Huang, DF,Lu, TG.

[11]Widespread 5-methylcytosine in the genomes of avian Coccidia and other apicomplexan parasites detected by an ELISA-based method. Gong, Zhenxing,Yin, Hao,Ma, Xueting,Liu, Baohong,Han, Zhenglan,Gou, Lingqiao,Cai, Jianping,Gong, Zhenxing,Yin, Hao,Ma, Xueting,Liu, Baohong,Han, Zhenglan,Gou, Lingqiao,Cai, Jianping,Gong, Zhenxing,Yin, Hao,Ma, Xueting,Liu, Baohong,Han, Zhenglan,Gou, Lingqiao,Cai, Jianping.

[12]Construction and Characterization of a Bacterial Artificial Chromosome Library from the Huoyan Goose. Hu, Peng Fei,Li, Xiang Chen,Chen, Xian Wei,Guan, Wei Jun,Ma, Yue Hui. 2012

[13]A Simple Sequence Repeat Marker Linked to the Susceptibility of Apple to Alternaria Blotch Caused by Alternaria alternata Apple Pathotype. Zhang, Liyi,Cong, Peihua,Li, Ying,Zhang, Zhen,Cheng, Zong-Ming,Cheng, Zong-Ming.

[14]Development of SSR molecular markers for Allium mongolicum. Hu, Jing,Hu, Xiaoke,Zhang, Jinhu,Fan, Baoli,Yu, Qiushi,Zhang, Qian.

[15]Molecular cloning and characterization of GhAPm, a gene encoding the mu subunit of the clathrin-associated adaptor protein complex that is associated with cotton (Gossypium hirsutum) fiber development. Zhou, Tao,Zhang, Rui,Yang, Dawei,Guo, Sandui.

[16]Response of the panicles exserted from the caulis and from various effective tillers at four stages of panicle development to neck blast in rice. Hao, Zhongna,Wang, Lianping,Liang, Jiangen,Tao, Rongxiang.

[17]The technology of large-scale pharmaceutical plasmid purification by cetyltrimethylammonium bromide and Tritonx-114. Hou, S. H.,Zhu, H. F.,Zhang, Q.,Yuan, W. F.,Sun, H. C.. 2010

[18]High-efficiency and stable genetic transformation of pear (Pyrus communis L.) leaf segments and regeneration of transgenic plants. Sun, Qingrong,Zhao, Yan,Sun, Hongyan,Hammond, Rose W.,Davis, Robert E.,Sun, Qingrong,Sun, Hongyan,Xin, Li.

[19]Karyotype analysis of Oreochromis mossambicus, O. urolepis hornorum and their hybrid based on Cot-1 DNA bands by fluorescence in situ hybridization. Zhu, Hua Ping,Lu, Mai Xin,Huang, Zhang Han,Gao, Feng Ying,Ma, Dong Mei,Zhou, Li,Gui, Jian Fang.

[20]The complete mitochondrial genome of Endangered fish Huso dauricus ( Acipenseriformes: Acipenseridae). Lu, Cuiyun,Gu, Ying,Li, Chao,Cheng, Lei,Sun, Xiaowen. 2016

作者其他论文 更多>>

微信小程序