Annotation and Analysis of Seven Viviparity-Related Genes in the Marine Fish - Rhacochilus vacca (Embiotocidae)

Investigation into the reproductive genes of non-mammalian species is under-represented in current scientific communities.  Such families as the viviparous Embiotocidae can provide valuable insight into the genetic understanding of reproductive processes because of its lesser-developed reproductive system comprised of a placenta-like structure or ovarian cavity.  Genomic research into the reproductive systems of species, such as the pile perch (Rhacochilus vacca), can further our understanding of the evolution of viviparity.  Because marginal consideration has been given to the study of viviparous fish species, this study aims to predict elements within the genome that specifically yield gene predictions and attach information to these predicated elements, such as biological functions and gene expressions.  This process, known as gene annotation, will lead to greater comprehension into the evolution of the lesser-developed ovarian cavity in other fish species. Furthermore, this will improve knowledge about the mammalian placenta because many of the genes produced by this study are conserved in mammals.  Using bioinformatic tools, such as MAKER, RepeatMasker, and tblastx we annotated reproductive genes of R.  vacca, which yielded seven candidate genes for further study. We tested for evidence of positive selection with PAML in these seven candidate genes. The annotation and subsequent analysis of the selection of the Embiotocoid reproductive genes provides insight into the evolutionary development of viviparity and increases our knowledge of developmental biology and the evolution of diverse life history strategies.