Vol.:(0123456789) 1 3 Genetica https://doi.org/10.1007/s10709-019-00067-1 ORIGINAL PAPER Compositional properties and codon usage pattern of mitochondrial ATP gene in diferent classes of Arthropoda Riazul Islam Barbhuiya 1  · Arif Uddin 2  · Supriyo Chakraborty 1 Received: 17 November 2018 / Accepted: 22 May 2019 © Springer Nature Switzerland AG 2019 Abstract Codon usage bias (CUB) is defned as the usage of synonymous codons unequally for an amino acid in a gene transcript. It is infuenced by both mutation pressure and natural selection and is a species-specifc property. In our current study, we used bioinformatic methods to investigate the coding sequences of mitochondrial adenosine triphosphate gene (MT-ATP) in diferent classes of arthropoda to know the codon usage pattern of the gene as no work was described earlier. The analysis of compositional properties suggested that the gene is AT rich. The efective number of codons revealed the CUB of both ATP6 and ATP8 gene was moderate. Heat map showed that the codons ending with AT were negatively associated with GC3 while the codons ending with GC were positively associated with GC3 in all the classes of arthropoda. Correspondence study revealed that the pattern of codon usage of ATP6 and ATP8 genes difered across classes. Neutrality plot suggested the codon usage bias of these two genes in phylum arthropoda was infuenced by both mutation pressure and natural selection. Keywords Codon usage bias · Mutation pressure · Natural selection · Arthropoda Introduction In a genetic code more than one codon often encodes a sin- gle amino acid and these codons are termed as synonymous codons for the amino acid except two amino acids in stand- ard code namely methionine and tryptophan (Baker et al. 1970). The mitochondrial DNA of arthropoda follows the translation Table 5 of NCBI. In this code, out of 64 codons, 62 codons encode 20 amino acids and the remaining two codons i.e. TAA and TAG act as termination signal. The amino acid serine is encoded by eight codons whereas both methionine and tryptophan amino acids are encoded by two codons each in this code unlike in the standard genetic code. The usage frequency of synonymous codons is not equal in coding sequences and this unequal frequency of codon usage leads to codon usage bias or CUB (Behura and Severson 2012). The unfairness in usage of codons confrms that the optimal codons, codons that are used repeatedly, can couple with the anticodons of the largely available tRNA genes (Sun et al. 2009). And it also tends to decrease the errors in processing and thereby reduces the chances of wrong inclusion of amino acids in a grow- ing polypeptide chain. It ensures a balancing situation amongst the efects of natural selection (includes selec- tion for translation, length and function of gene), mutation pressure (includes GC content and position of mutation in base) and random genetic drift (Bulmer 1991; Sharp and Li 1986a). Codon bias is a unique feature of the genome of an organism and among the genes of the same organism; it may vary signifcantly (Grantham et al. 1980; Marin et al. 1989; Prat et al. 2009a). It is well obvious that the variation in codon usage within the same family of syn- onymous codon governs the translational efciency of a gene, thus having a strong impact in framing the genome evolution (Bentele et al. 2013). The up surged transla- tional efciency assists organisms to ft into the dynamic environmental conditions and is often correlated with their lifestyle (Botzman and Margalit 2011). Previously, Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10709-019-00067-1) contains supplementary material, which is available to authorized users. * Supriyo Chakraborty supriyoch_2008@redifmail.com 1 Department of Biotechnology, Assam University, Silchar, Assam 788011, India 2 Department of Zoology, Moinul Hoque Choudhury Science College, Algapur, Hailakandi, Assam 788150, India