Contents lists available at ScienceDirect Molecular & Biochemical Parasitology journal homepage: www.elsevier.com/locate/molbiopara Preference of A/T ending codons in mitochondrial ATP6 gene under phylum Platyhelminthes Codon usage of ATP6 gene in Platyhelminthes Gulshana A Mazumder a , Arif Uddin b , Supriyo Chakraborty a, ⁎ a Department of Biotechnology, Assam University, Silchar, 788011, Assam, India b Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India ARTICLE INFO Keywords: Codon usage bias Mutation pressure Natural selection and synonymous codon usage order ABSTRACT Unequal usage of synonymous codons in the gene transcript for an amino acid is known as codon usage bias (CUB). It is a unique property of gene as well as genome. Mutation and natural selection are known to be the major factors that influence CUB. Other factors encompass gene expression level, GC content, codon position, recombination rate, RNA stability and gene length. CUB analysis helps in in-depth understanding of the mole- cular biology, genetics and genome evolution in a species. We used bioinformatic methods to explore the pattern of CUB in MT-ATP6 gene in different classes of platyhelminthes. The analysis is based on genetic code of translational table 14 of National Center of Biotechnology Information (NCBI) where the codon AAA codes for asparagine and TAA for tyrosine amino acid. The synonymous codon usage order (SCUO), an index of CUB, values in different classes namely cestoda, monogenea, rabditophora, trematoda and turbellaria of platy- helminths were found to be 0.43, 0.32, 0.49, 0.40 and 0.36, respectively which suggest that the codon usage bias of ATP6 gene was low (SCUO < 0.50). Highly significant correlation (p < 0.001) was found between SCUO and various GC contents indicating that GC composition had an influence on CUB. From the relative synonymous codon usage (RSCU) analysis on codons, we found most of the over-represented codons in all the classes were A/ T ending types, which suggested that the preferred codons were influenced by compositional constraints. The PR2 plot revealed asymmetric usage of AT and GC bases among the four fold degenerate codon families with greater usage of G and T over A and C. Highly significant correlation (p < 0.001) was found between overall nucleotide composition and its 3rd codon position suggesting that both natural selection and mutation pressure might have influenced the CUB among different classes. Neutrality analysis revealed that natural selection might play a major role. Mutational responsive index (MRI) and translational selection (P2) values elucidated that selection for translational efficiency moderately affected the codon usage bias in MT-ATP6 gene. 1. Introduction Unlike standard genetic code the mitochondrial genetic code of phylum Platyhelminthes follows the genetic code given in translation table 14 of NCBI. It consists of 63 sense codons and a single stop codon (TAG), and 18 amino acids are encoded by of 2–8 synonymous codons. The amino acid serine is encoded by 8 codons and both asparagine and tyrosine are encoded by 3 codons each. Amino acid tryptophan is en- coded by 2 codons whereas lysine and methionine are encoded by one codon each. This genetic code is uniquely characterized by AAA codon encoding asparagine and TAA codon encoding tyrosine [1]. In 1960s, the idea cropped out that most of amino acids were coded by more than one codon (2–6), with difference at the third codon position. Later in 1980’s with the introduction of whole genome se- quencing, it was stated that synonymous codons are not used in equal frequency in mRNA molecules [2]. Codons which encode the same amino acid are known as synonymous codons, and the usage of these codons in an mRNA is a non-random process. The phenomenon wherein some codons are used more often than others within the same family leads to the manifestation of codon usage bias (CUB) [3,4]. Numerous studies revealed that codon usage pattern is mainly influenced by natural selection and mutational pressure [5–8]. CUB might play an important role in modulating the expression level of exogenous genes in a genome and also in predicting the optimum host range of the exo- genous genes [9]. Various factors that influence the codon usage bias in different https://doi.org/10.1016/j.molbiopara.2018.08.007 Received 20 May 2018; Received in revised form 17 August 2018; Accepted 22 August 2018 ⁎ Corresponding author. E-mail address: supriyoch_2008@rediffmail.com (S. Chakraborty). Molecular & Biochemical Parasitology 225 (2018) 15–26 Available online 24 August 2018 0166-6851/ © 2018 Elsevier B.V. All rights reserved. T