Analysis of codon usage bias of chloroplast genes in Oryza species
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ORIGINAL ARTICLE
Analysis of codon usage bias of chloroplast genes in Oryza species Codon usage of chloroplast genes in Oryza species Supriyo Chakraborty1 · Sophiarani Yengkhom1 · Arif Uddin2 Received: 25 March 2020 / Accepted: 15 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
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 1.6) among 59 synonymous codons
in O. longistaminata, seven codons in O. australiensis, six codons in O. meridionalis and O. officinalis, five codons in O. alta, O. glaberrima, O. sativa var. Indica, and O. sativa var. Japonica, four codons in O. barthii, O. eichingeri, O. glumipatula, O. grandiglumis, O. latifolia, O punctata, O. rhizomatis, and O. rufipogon, and three codons in O. minuta, whereas two codons were found to be over-represented in O. nivara.
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Table 2 t test among compositional properties in different Oryza species
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Table 2 (continued)
*Significant at the 0.05 level (two-tailed) (shown in blue color); **Significant at the 0.01 level (two-tailed) (shown in black and green colors); non-significant t tests are shown in red colors.
Mutational pressure versus natural selection in CUB of cp genes of Oryza We estimated the Karl Pearson’s correlation coefficients between overall nucleotide composition (A%, T%, G%, C%, and GC%) and nucleotide composition at the third
codon position (A%, T3%, G3%, C3%, and GC3%) to explore the factors influencing the codon usage pattern in the cp CDS of Oryza (Table 3). In all the 18 Oryza species, highly significant positive correlation was observed between
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