Synonymous Codon Usage, GC3, and Evolutionary Patterns Across Plastomes of Three Pooid Model Species: Emerging Grass Genome Models for Monocots
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We have analyzed factors affecting the codon usage pattern of the chloroplasts genomes of representative species of pooid grass family. Correspondence analysis of relative synonymous codon usages (RSCU) showed that genes on secondary axis were correlated with their GC3S values (all r > 0.3, p < 0.05), indicating mutational bias as an important selective force that shaped the variation in the codon usage among chloroplast genes. The Nc-plot showed that although a majority of the points with low-Nc values were lying below the expected curve, a few genes lied on the expected curve. Nc plot clearly showed that mutational bias plays a major role in codon biology across the monocot plastomes. The hydrophobicity and aromaticity of encoded proteins of each species were found to be other factors of codon usage variation. In the view of above light, besides natural selection, several other factors also likely to be involved in determining the selective constraints on codon bias in plastomes of pooid grass genomes. In addition, five codons (B. distachyon), seven codons (H. vulgare), and four codons (T. aestivum) were identified as optimal codons of the three grass chloroplasts. To identify genes evolving under positive selection, rates of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) were computed for all groups of orthologous gene pairs.
KeywordsBrachypodium distachyon Triticum aestivum Hordeum vulgare subsp. vulgare Correspondence analysis GC3 biology Mutational bias
Gaurav Sablok thanks Key Lab of Horticultural Plant Biology (MOE), Huazhong Agricultural University. Tsuyoshi Hachiya and Yasubumi Sakakibara of Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Japan are gratefully acknowledged for chrom-link visualization of the genomes. We gratefully acknowledge Professor Hans K. Stenoien, Systematics & Evolution Group, Norwegian University of Science and Technology, Norway for providing the peer review eye during the manuscript preparation. This work was supported by the Department of Biotechnology, Ministry of Science and Technology, Government of India. Research work of F. Vazquez is supported by an Ambizione Grant (PZ00P3_126329/1 to F.V.) of the Swiss National Science Foundation. Tatiana Tatarinova would like to thank the University of Glamorgan’s Research Investment Scheme for supporting this project.
- 1.Sau, K., & Deb, A. (2008). Temperature influences synonymous codon and amino acid usage biases in the phages infecting extremely thermophilic prokaryotes. In Silico Biology, 9, 0001.Google Scholar
- 20.Zhang, W. J., Zhou, J., Li, Z. F., Wang, L., Gu, X., & Zhong, Y. (2007). Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. Journal of Integrative Plant Biology, 149, 37–44.Google Scholar
- 23.Greenacre, M. J. (1984). Theory and application of correspondence analysis (p. 223). London: Academic Press.Google Scholar
- 26.Kyte, J., & Doolittle, R. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Evolution, 157, 105–132.Google Scholar
- 28.Ikemura, T. (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 2, 13–34.Google Scholar
- 34.Sakakibara, Y., Osana, Y., & Popendorf, K. (2007). Development of a large-scale comparative genome system and its application to the analysis of mycobacteria genomes. Nihon Hansenbyo Gakkai Zasshi, 76, 251–256.Google Scholar
- 41.Sharp, P. M., Cowe, E., Higgins, D. G., Shields, D. C., Wolfe, K. H., & Wright, F. (1988). Codon usage in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Research, 16, 8207–8711.CrossRefGoogle Scholar
- 42.Knight, R. D., Freeland, S. J., & Landweber, L. F. (2001). A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biology, 2, 0010.1–0010.13.Google Scholar
- 44.Hasegawa, M., Cao, Y., & Yang, Z. (1998). Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species. Molecular Biology and Evolution, 15, 1499–1505.Google Scholar
- 50.Xia, X. (1998). How optimized is the translational machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae? Genetics, 149, 37–44.Google Scholar
- 56.Selvaraj, D., Sarma, R. K., & Sathishkumar, R. (2008). Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding. Bioinformation, 3, 24–27.Google Scholar