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Analysis of codon usage bias of chloroplast genes in Oryza species

Codon usage of chloroplast genes in Oryza species

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Abstract

Main conclusion

The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural selection.

Abstract

Codon usage bias (CUB) is the unequal usage of synonymous codons in which some codons are more preferred to others in the coding sequences of genes. It shows a species-specific property. We studied the patterns of codon usage and the factors that influenced the CUB of protein-coding chloroplast (cp) genes in 18 Oryza species as no work was yet reported. The nucleotide composition analysis revealed that the overall GC content of cp genes in different species of Oryza was lower than 50%, i.e., Oryza cp genes were AT rich. Synonymous codon usage order (SCUO) suggested that CUB was weak in the cp genes of different Oryza species. A highly significant correlation was observed between overall nucleotides and its constituents at the third codon position suggesting that both, mutation pressure and natural selection, might influence the CUB. Correspondence analysis (COA) revealed that codon usage pattern differed across Oryza species. In the neutrality plot, a narrow range of GC3 distribution was recorded and some points were diagonally distributed in all the plots, suggesting that natural selection and mutation pressure might have influenced the CUB. The slope of the regression line was < 0.5, augmenting our inference that natural selection might have played a major role, while mutation pressure had a minor role in sha** the CUB of cp genes. The magnitudes of mutation pressure and natural selection on cp genes varied across Oryza species.

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Abbreviations

COA:

Correspondence analysis

cp:

Chloroplast

CUB:

Codon usage bias

MILC:

Measure independent of length and composition

PR2:

Parity rule 2

RSCU:

Relative synonymous codon usage

SCUO:

Synonymous codon usage order

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Acknowledgements

The authors are thankful to Assam University, Silchar, India for providing the necessary facilities. The work was not funded by any agency.

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Authors and Affiliations

  1. Department of Biotechnology, Assam University, Silchar, 788011, Assam, India

    Supriyo Chakraborty & Sophiarani Yengkhom

  2. Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India

    Arif Uddin

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  1. Supriyo Chakraborty
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Correspondence to Supriyo Chakraborty.

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Chakraborty, S., Yengkhom, S. & Uddin, A. Analysis of codon usage bias of chloroplast genes in Oryza species. Planta 252, 67 (2020). https://doi.org/10.1007/s00425-020-03470-7

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