Genome-wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus Bombina
| Autor: | Supriyo Chakraborty, Arif Uddin, Parvin A. Barbhuiya |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
0301 basic medicine Bombina bombina Bombina maxima 010603 evolutionary biology 01 natural sciences Bombina variegata 03 medical and health sciences Species Specificity Genetics Animals Codon Usage Ecology Evolution Behavior and Systematics Phylogeny biology Phylogenetic tree Computational Biology Genetic Variation biology.organism_classification Bombina lichuanensis Biological Evolution 030104 developmental biology Genes Mitochondrial Evolutionary biology Codon usage bias Mutation Molecular Medicine Animal Science and Zoology Bombina orientalis Anura GC-content Developmental Biology Genome-Wide Association Study |
| Zdroj: | Journal of experimental zoology. Part B, Molecular and developmental evolution. 332(3-4) |
| ISSN: | 1552-5015 |
| Popis: | The biological phenomenon where some synonymous codons are repeatedly preferred to others in gene transcripts is called codon usage bias (CUB). The analysis of CUB is not only helpful in evolutionary biology but also in improving the expression level of exogenous genes in the host cell by codon optimization. The overall nucleotide composition analysis demonstrated an unequal distribution of four nucleobases and T% was the highest in all seven species. The genes were AT-rich, evident from overall low GC content. In addition, third codon position analysis indicated that in four Bombina species namely, Bombina fortinuptialis, Bombina lichuanensis, Bombina maxima, Bombina microdeladigitora, nucleobase A3/T3 was the preferred one, whereas A3/C3 was favored in Bombina bombina, Bombina orientalis, and Bombina variegata. Influence of mutation pressure on codon distribution and codon bias was evident from correlation analysis. Correspondence analysis demonstrated that compositional bias driven by mutation pressure along with natural selection acted on CUB of mitochondrial genes. Neutrality plot revealed that natural selection played a major role whereas mutation pressure had a minor but significant role. Our phylogenetic analyses showed that closely linked species belonging to the same genus were noticeably separated in different clades. |
| Databáze: | OpenAIRE |
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