FULL LENGTH RESEARCH PAPER Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects C. SELVA KUMAR 1 , RAHUL R. NAIR 2 , K. G. SIVARAMAKRISHNAN 3 , D. GANESH 4 , S. JANARTHANAN 1 , M. ARUNACHALAM 5 , & T. SIVARUBAN 6 1 Department of Zoology, University of Madras, Chennai 600 025, Tamil Nadu, India, 2 Department of Biotechnology, Sri Paramakalyani Centre for Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627412, Tamil Nadu, India, 3 Department of Zoology, Madras Christian College, Tambaram East, Chennai 600 059, Tamil Nadu, India, 4 Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India, 5 Sri Paramakalyani Centre for Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627412, Tamil Nadu, India, and 6 Department of Zoology, The American College, Madurai 625002, Tamil Nadu, India (Received 3 February 2012; revised 3 July 2012; accepted 3 July 2012) Abstract Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat – microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages. Keywords: Aquatic insects, relative synonymous codon usage, Ephemeroptera, Plecoptera, Odonata, mitochondrial DNA Introduction When the genetic code was deciphered in the 1960s, it became very clear that most amino acids are encoded by multiple codons, typically differing only at the third position of the codon, i.e. synonymous codons (Sharp et al. 2010). There are a total of 64 codons, with 61 of them coding for 20 different amino acids and the remaining three serving as stop codons. Usage of synonymous codons is not at equal frequencies both within and between organisms (Grantham et al. 1980; Liu et al. 2011; Sablok et al. 2011; Xu et al. 2011). The trends in synonymous codon usage (SCU) ISSN 1940-1736 print/ISSN 1940-1744 online q 2012 Informa UK, Ltd. DOI: 10.3109/19401736.2012.710203 Correspondence: K. G. Sivaramakrishnan, Department of Zoology, Madras Christian College, Tambaram East, Chennai 600 059, Tamil Nadu, India. Tel: þ 91 9940490259. Fax: þ 91-44-22352494/3309. E-mail: kgskrishnan@gmail.com Mitochondrial DNA, December 2012; 23(6): 447–460 Mitochondrial DNA Downloaded from informahealthcare.com by IBI Circulation - Ashley Publications Ltd on 03/07/13 For personal use only.