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Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities

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Abstract

The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydrophobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypothesis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebacterium. The study reveals close relationship between non-pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism.

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Acknowledgements

SP acknowledges DBT, Govt. of India for creation of Bioinformatics Infrastructure Facility at Vidyasagar University and DBT, Govt. of West Bengal for funding. IS and AR acknowledge UGC-BSR and CSIR respectively. AS is grateful to DBT, Govt. of India for creating Bioinformatics Facility at NBU.

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Authors and Affiliations

  1. Bioinformatics Infrastructure Facility, Department of Microbiology, Vidyasagar University, Midnapore, 721 102, India

    Shilpee Pal, Pradeep K. Das Mohapatra & Keshab C. Mondal

  2. Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling, 734 013, India

    Indrani Sarkar, Ayan Roy & Arnab Sen

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  1. Shilpee Pal
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  2. Indrani Sarkar
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Correspondence to Arnab Sen.

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Pal, S., Sarkar, I., Roy, A. et al. Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities. Genetica 146, 13–27 (2018). https://doi.org/10.1007/s10709-017-9986-6

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  • DOI: https://doi.org/10.1007/s10709-017-9986-6

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