Abstract
Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism's genome (such as the mouse genome) in order to make physiological inferences about the role of genes and proteins in a less characterized organism's genome (such as the Burmese python). We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. 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. Additional enhancements to reptile genomic resources will further enhance their value.
Highlights
Reptiles represent a diverse and biologically distinct group of vertebrates for which most species have yet to be systematically studied
We identified a set of P. regius sequences for which orthologous P. bivittatus sequences were available
To explore the possibility that P. regius and P. bivittatus exhibit sufficient genetic similarity to justify using one species as a genetic model for the other species, we assessed the level of sequence identity among a set of protein coding sequences, mitochondrial DNA sequences, and protein sequences
Summary
Reptiles represent a diverse and biologically distinct group of vertebrates for which most species have yet to be systematically studied. It is worth noting that reptiles are of ecological interest as both endangered and invasive species. In 2015, California Department of Fish and Wildlife listed ten distinct reptile species as either endangered or threatened, including four species of snakes: Charina bottae (southern rubber boa), Thamnophis gigas (giant garter snake), Thamnophis sirtalis tetrataenia (San Francisco garter snake), and Masticophis lateralis euryxanthus (alameda whipsnake). California Department of Fish and Wildlife classifies other reptiles as invasive species, such as Nerodia fasciata (southern watersnake). Deciphering reptile reproductive biology can provide avenues for facilitating successful breeding in endangered species and, at the same time, may offer insights into reducing the reproduction of invasive species
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