Comparative Genomics Analysis Identifies Genes Associated with Reproductive Phenotypes in Burmese Python (Python bivittatus)

Comparative genomics approaches leverage functional genomics knowledge from one genome (such as mouse) to make inferences about the role of genes and proteins in a less characterized genome (such as the Burmese python). We describe an in-silico comparative genomics approach aimed at identifying genes within the python genome that are likely to be associated with male reproductive phenotypes. From among a set of orthologous genes associated with sperm biology, we leverage multiple sequence alignments to identify phylogenetic relationships among mammalian, avian, reptilie and invertebrate  taxa. We next systematically characterize the association of python sequences with gene ontology annotation and biological pathways from the KEGG database rsulting in the identification of 129 gene-phenotype relationships across 98 genes encoded in the python genome which are implicated in 10 specific sperm phenotypes. We also identified twenty-three python ortholgous genes associated with pigmentation and coat color in mammals and describe pair-wise protein sequence identity between a variety of species. Some of the pleiotropic effects associated with these 23 genes include reproductive phenotypes, such as phenotypic associations of OCA2 with spermiogenesis, KIT with sterility and KIT-LG with sterility. Together, these newly annotated Python bivittatus genome resources provide a enhanced understanding of the biology relating to reptile spermatogenesis, fertility and reproduction. Applications of our research include: (1) production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2) enhanced assisted reproduction technology for endangered and captive reptiles; and (3) novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles.