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

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA. .
BMC Research Notes 08/2011; 4(1):310. DOI: 10.1186/1756-0500-4-310
Source: PubMed


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.
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.
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.

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    • "The phylogenetic position of this latter species is particularly important, as it lies outside of the proposed clade of ancestrally venomous reptiles (the Toxicofera (Fry et al. 2006; Fry et al. 2009a; Fry et al. 2012b; Fry et al. 2013)) and therefore genes found in the salivary gland of this species can be taken to represent the ancestral squamate expression pattern. We also take advantage of available transcriptomic resources for body tissues in a number of other reptile species, including king cobra (Ophiophagus hannah) venom gland, accessory gland and pooled tissues (heart, lung, spleen, brain, testes, gall bladder, pancreas, small intestine, kidney, liver, eye, tongue and stomach) (Vonk et al. 2013), garter snake (Thamnophis elegans) liver (Schwartz and Bronikowski 2013) and pooled tissue (brain, gonads, heart, kidney, liver, spleen and blood of males and females) (Schwartz et al. 2010), Burmese python (Python molurus bivittatus) pooled heart and liver (Castoe et al. 2011) and corn snake brain (Tzika et al. 2011). "
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    ABSTRACT: Snake venom has been hypothesised to have originated and diversified via a process that involves duplication of genes encoding body proteins with subsequent recruitment of the copy to the venom gland, where natural selection acts to develop or increase toxicity. However, gene duplication is known to be a rare event in vertebrate genomes and the recruitment of duplicated genes to a novel expression domain (neofunctionalisation) is an even rarer process that requires the evolution of novel combinations of transcription factor binding sites in upstream regulatory regions. Therefore, whilst this hypothesis concerning the evolution of snake venom is therefore very unlikely and should be regarded with caution, it is nonetheless often assumed to be established fact, hindering research into the true origins of snake venom toxins. To critically evaluate this hypothesis we have generated transcriptomic data for body tissues and salivary and venom glands from five species of venomous and non-venomous reptiles. Our comparative transcriptomic analysis of these data reveals that snake venom does not evolve via the hypothesised process of duplication and recruitment of genes encoding body proteins. Indeed, our results show that many proposed venom toxins are in fact expressed in a wide variety of body tissues, including the salivary gland of non-venomous reptiles and that these genes have therefore been restricted to the venom gland following duplication, not recruited. Thus snake venom evolves via the duplication and subfunctionalisation of genes encoding existing salivary proteins. These results highlight the danger of the elegant and intuitive "just-so story" in evolutionary biology.
    Genome Biology and Evolution 07/2014; 6(8). DOI:10.1093/gbe/evu166 · 4.23 Impact Factor
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    • "which include green anole (Anolis carolinensis), chicken (Gallus gallus), human (Homo sapiens), opossum (Monodelphis domestica), zebra finch (Taeniopygia guttata), and western clawed frog (Xenopus tropicalis). Additionally, we downloaded transcriptomic data of the soft-shelled turtle (Pelodiscus sinensis), Nile crocodile (Crocodylus niloticus), royal python (Python regius), and tuatara (Sphenodon punctatus) [1], [66]–[68]. After adding the Chinese pond turtle, our dataset included a total of 11 species, and had at least two representatives of each major lineage of living amniotes (with the exception of a single crocodilian). "
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    ABSTRACT: The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.
    PLoS ONE 11/2013; 8(11):e79348. DOI:10.1371/journal.pone.0079348 · 3.23 Impact Factor
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    • "Notably, the various biological processes in our analysis are more evenly distributed than those found recently in a python (P. molurus bivittatus) transcriptome analysis (Castoe et al. 2011). We interpret this result as possible differences in the sampled tissues in our and the python studies. "
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