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Synonymous Codon Usage, GC(3), and Evolutionary Patterns Across Plastomes of Three Pooid Model Species: Emerging Grass Genome Models for Monocots

Sablok, G. and Nayak, K. C. and Vazquez, F. and Tatarinova, T. V.. (2011) Synonymous Codon Usage, GC(3), and Evolutionary Patterns Across Plastomes of Three Pooid Model Species: Emerging Grass Genome Models for Monocots. Molecular Biotechnology, 49 (2). pp. 116-128.

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Official URL: http://edoc.unibas.ch/dok/A6308445

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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 GC(3S) 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.
Faculties and Departments:05 Faculty of Science > Departement Umweltwissenschaften > Botanik > Pflanzenphysiologie Pathogenabwehr (Boller)
UniBasel Contributors:Vazquez, Franck
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:Springer
ISSN:1073-6085
e-ISSN:1559-0305
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:18 Jan 2018 10:13
Deposited On:07 Nov 2014 08:29

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