A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)

<p>Abstract</p> <p>Background</p> <p>Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, including those related to development, metabolism, physiology, and venom. Despite their importance as research models, genomic resources for snakes are few. Among snakes, the Burmese python is the premier model for studying extremes of metabolic fluctuation and physiological remodelling. In this species, the consumption of large infrequent meals can induce a 40-fold increase in metabolic rate and more than a doubling in size of some organs. To provide a foundation for research utilizing the python, our aim was to assemble and annotate a transcriptome reference from the heart and liver. To accomplish this aim, we used the 454-FLX sequencing platform to collect sequence data from multiple cDNA libraries.</p> <p>Results</p> <p>We collected nearly 1 million 454 sequence reads, and assembled these into 37,245 contigs with a combined length of 13,409,006 bp. To identify known genes, these contigs were compared to chicken and lizard gene sets, and to all Genbank sequences. A total of 13,286 of these contigs were annotated based on similarity to known genes or Genbank sequences. We used gene ontology (GO) assignments to characterize the types of genes in this transcriptome resource. The raw data, transcript contig assembly, and transcript annotations are made available online for use by the broader research community.</p> <p>Conclusion</p> <p>These data should facilitate future studies using pythons and snakes in general, helping to further contribute to the utilization of snakes as a model evolutionary and physiological system. This sequence collection represents a major genomic resource for the Burmese python, and the large number of transcript sequences characterized should contribute to future research in this and other snake species.</p

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes

The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes

The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline.This article is from Genome Biology 12 (2011): 406, doi: 10.1186/gb-2011-12-7-406. Posted with permission.</p

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. Results Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.Dentistry, Faculty ofNon UBCReviewedFacult

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Abstract Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species’ physiological capacities to withstand extreme anoxia and tissue freezing. Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle’s extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders. Keywords: Amniote phylogeny, anoxia tolerance, chelonian, freeze tolerance, genomics, longevity, phylogenomics, physiology, turtle, evolutionary ratesThis is an article from Genome Biology 14 (2013): 1, doi:10.1186/gb-2013-14-3-r28. Posted with permission.</p