Synonymous codon usage in chloroplast genome of Coffea arabica



Rahul R Nair2, Manivasagam B Nandhini1, Elango Monalisha1, Kavitha Murugan2, Thilaga Sethuraman2, Sangeetha Nagarajan2, Nayani Surya Prakash Rao3 & Doss Ganesh1*



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; *Corresponding author


Article Type




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.



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



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

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P Kangueane






Biomedical Informatics



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