Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects

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

Acknowledgements

We thank an anonymous reviewer for valuable suggestions for improving the analysis and writing. We are grateful to Mr Li Hu, Department of Entomology, China Agricultural University, China for his critical inputs in the manuscript. We thank Dr M. Muralidharan, Sri Paramakalyani Centre for Environmental Sciences, Manonmaniam Sundaranar University, India for his help in statistical analysis.

Declaration of interest The first author would like to thank University Grants Commission, New Delhi, India for providing Dr D. S. Kothari Post Doctoral Fellowship (No. F.4-2/2006 (BSR) /13-670/2012 (BSR). K. G. Sivaramakrishnan thanks University Grants Commission, New Delhi, India for the award of Emeritus Fellowship (No. F.6-39/2011 (SA-II). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.