Title

Authors

Affiliation

¹Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar 625 021, Madurai, Tamil Nadu, India; ²Plant Genetic Improvement Laboratory, Department of Biotechnology, SPK Centre for Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627 412, Tirunelveli District, Tamil Nadu. India; ³Division of Plant Breeding, Central Coffee Research Institute, Coffee Research Station Post 577 117, Chikmagalur District, Karnataka, India.

Email

ganeshdsneha@yahoo.co.in; *Corresponding author

Article Type

Hypothesis

Date

Received October 22, 2012; Accepted October 26, 2012; Published November 13, 2012

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A3, T3, G3, C3, GC3) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC3 plot grouped majority of the analyzed genes on or just below the left side of the expected GC3 curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.

Keywords

Coffea arabica, Synonymous codon usage, ENC Vs GC3 plot, Codon adaptation index, Correspondence analysis.

Citation

Nair et al. Bioinformation 8(22): 1096-1104 (2012)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.