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Synonymous Codon Usage, GC3, and Evolutionary Patterns Across Plastomes of Three Pooid Model Species: Emerging Grass Genome Models for Monocots

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Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. Key Lab of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070, Shizishan, China

    Gaurav Sablok

  2. Department of Biotechnology, Bioinformatics Centre, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751 023, India

    Kinshuk Chandra Nayak

  3. Zurich-Basel Plant Science Center, Botanical Institute, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland

    Franck Vazquez

  4. Division of Mathematics and Statistics, University of Glamorgan, Pontypridd, CF37 1DL, UK

    Tatiana V. Tatarinova

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  1. Gaurav Sablok
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  2. Kinshuk Chandra Nayak
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  4. Tatiana V. Tatarinova
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Correspondence to Gaurav Sablok or Tatiana V. Tatarinova.

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Sablok, G., Nayak, K.C., Vazquez, F. et al. Synonymous Codon Usage, GC3, and Evolutionary Patterns Across Plastomes of Three Pooid Model Species: Emerging Grass Genome Models for Monocots. Mol Biotechnol 49, 116–128 (2011). https://doi.org/10.1007/s12033-011-9383-9

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