The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization
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  • 作者：Yun Xia (14)
    Yuchi Zheng (14)
    Ikuo Miura (15)
    Pamela BY Wong (16)
    Robert W Murphy (16)
    Xiaomao Zeng (14)

    14. Chengdu Institute of Biology     ; Chinese Academy of Sciences ; Chengdu ; 610041 ; China
    15. Insititute for Amphibian Biology     ; Graduate School of Science ; Hiroshima University ; Kagamiyama 1-3-1 ; Higashi-Hiroshima ; 739-8526 ; Japan
    16. Centre for Biodiversity and Conservation Biology     ; Royal Ontario Museum ; 100 Queen鈥檚 Park ; Toronto ; ON ; M5S 2C6 ; Canada
  • 关键词：Mitogenomics ; tRNA gene ; Gene rearrangement ; Gene duplication ; Random gene loss ; Gene order
  • 刊名：BMC Genomics
  • 出版年：2014
  • 出版时间：December 2014
  • 年：2014
  • 卷：15
  • 期：1
  • 全文大小：2,617 KB
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  • 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
  • 出版者：BioMed Central
  • ISSN：1471-2164
文摘
Background Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage. Results Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and dN/dS ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated. Conclusions No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations.

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