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Evolutionary direction of processed pseudogenes

中国科学：生命科学英文版 2016年第8期59卷 839-849页

作者： Guoqing Liu Xiangjun Cui Hong Li Lu Cai School of Life Science and Technology Inner Mongolia University of Science and TechnologyBaotou 014010China 1nstitute of Bioengineering and Technology lnner Mongolia University of Science and TechnologyBaotou 014010China School of Physical Science and Technology Inner Mongolia UniversityHohhot 010021China Computational Systems Biology Lab Department of Biochemistry and Molecular BiologyInstitute of BioinformaticsUniversity of GeorgiaAthens GA 30602USA

While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection.

关键词： GC content mutual information transcription factor binding motifs mutational bias recombination

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Analysis of synonymous codon usage in 11 Archaeal Virus genomes

Analysis of synonymous codon usage in 11 Archaeal Virus geno...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Sen Li Jie Yang State Key Laboratory of Pharmaceutical Biotechnology School of Life ScienceNanjing University Department of Biochemistry Nanjing University

Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes.Archaeal Viruses isolated from these hot habitats usually have double-stranded DNA genomes,linear or circular,and can infect members of the Archaea domain.In this study,the codon usage bias and dinucleotide composition in the available complete Archaeal Virus genome sequences have been investigated.It was found that there is a significant variation in codon usage bias among different Archaeal Virus species,which is mainly determined by the base composition.The outcome of correspondence analysis (COA) and Spearman’s rank correlation analysis shows that codon usage of selected Archaeal Virus genes depends mainly on GC richness of genome,and the gene’s function,albeit with smaller effects,also contributes to codon usage in this virus.Furthermore,this investigation reveals that aromaticity of each protein is also critical in affecting codon usage bias of these viral genes although it was less important than that of the mutational bias.Finally,the relative synonymous codon usage(RSCU) of 26 genes from these 11 Archaeal Virus genomes is analyzed using a hierarchical cluster method.The result reveals that genes of genomes with similar GC content are classified into the same lineage,and gene function may play important role in determining the classification at the level of sublineage although other factors may also involve in.These conclusions not only can offer an insight into the codon usage bias of Archaeal Virus,but also may help in the gene classification of Archaeal Viruses.

关键词： Archaeal Virus Synonymous codon usage mutational bias Gene function Hierarchical cluster analysis

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