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Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

文献类型： 外文期刊

作者： Qi, Yueying 1 ; Xu, Wenjing 1 ; Xing, Tian 1 ; Zhao, Mingming 1 ; Li, Nana 2 ; Yan, Li 1 ; Xia, Guangmin 1 ; Wang, Mengch 1 ;

作者机构： 1.Shandong Univ, Sch Life Sci, Key Lab Plant Cell Engn & Germplasm Innovat, Minist Educ, Jinan 250100, Shandong, Peoples R China

2.Shandong Ctr Crop Germplasm Resources, Jinan 250100, Shandong, Peoples R China

关键词： plastid;synonymous codon usage bias;plant taxonomy;intron number;exon position;DNA methylation

期刊名称：EVOLUTIONARY BIOINFORMATICS （ 影响因子：1.625； 五年影响因子：2.38 ）

ISSN： 1176-9343

年卷期： 2015 年 11 卷

页码：

收录情况： SCI

摘要： Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A-and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation-induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.

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