Insight of genetic features prevalent in three Echinoderm species (Apostichopus japonicus, Heliocedaris erythrogramma and Asterias rubens) and their evolutionary association using comparative codon pattern analysis

Abstract

With the increasing accumulation of genomic sequence information of echinoderms, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern among three echinoderm species Heliocidaris erythrogramma (Sea urchin), Apostichopus japonicus (Sea cucumber) and Asterias rubens (Star fish) belonging to similar habitats. We performed detailed comparative analysis of echinodermal genomes with respect to codon bias. Our analysis reflects that the genome of H. erythrogramma and A. rubens was found to be GC rich, whereas the genome of A. japonicus was found to be AT rich. The RSCU (Relative usage of synonymous codons) analysis revealed dominance of A- and/or C-ending codons in H. erythrogramma and A. rubens while A- and/or U-ending codons were preferred in A. japonicus. Overall, a weak codon bias was prevailed in all the three genomes of selected echinoderm species. The main influencing elements in developing codon usage bias (CUB) appeared to be mutational pressure and natural selection. Despite sharing the same ecological habitat and functional features, CUB analysis revealed a close relationship between H. erythrogramma and A. rubens among the three Echinoderm species chosen for this study. The present study will be helpful in understanding the genetic features prevalent in Echinoderms and would lay a foundation for future research on other Echinoderm species.