REPTILIAN TRANSCRIPTOMES
Next-Generation Sequencing of Reptilian Transcriptomes
“Reptilian-transcriptomes.org” originated in the Laboratory of Artificial & Natural Evolution (LANE) at the University of Geneva (Switzerland) and is funded by the Swiss National Science Foundation. The major aim of the project is to provide transcriptome sequence assemblies from various organs in reptilian species, but also microsatellite loci, as well as SNP and indel polymorphisms for population genetics and linkage analyses. This resource should prove useful for the genomic and herpetology communities alike, as reptiles are becoming important new models for comparative genomics, ecology, and evolutionary developmental genetics. Indeed, among under-represented groups, in terms of genome sequence data, are the major lineages of Reptilia, which diverged 200-280 million years ago: Testudines (turtles, tortoises, and terrapins), Lepidosauria (the tuatara, lizards, and snakes) and Archosauria (crocodiles and birds). Even if we exclude the 10,000 extant species of birds, Reptilia still includes over 8,000 species (compared to 5,400 species of mammals) which display a remarkable range of life histories, sex-determining systems, reproductive modes, physiologies, and body plans. Hence, comparative genomic analyses incorporating reptilian genomes promise to uncover evolutionary novelties more diverse in many respects than those revealed by genomic comparisons among mammals. Furthermore, non-avian reptilian genomes would greatly improve the comparison between mammals and birds by incorporating the major missing nodes between these two lineages. Even if next-generation methods make the sequencing of a complex genome possible in a matter of weeks, such a project remains very costly and requires much additional time for assembly and annotation. For species that are much divergent from existing high-quality genomes, gene identification and annotation greatly benefits from transcriptome data. Again, next-generation sequencing will probably become the method of choice for generating high-quality transcriptome data.
Brain Transcriptomes
We first chose to focus on the brain transcriptome for two reasons:
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1.The brain exhibits one of the most complex (i.e., diverse) transcriptomes of all organs in vertebrates; hence, it is a tissue of choice for sequencing a maximum number of transcripts while reducing the need for normalization;
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2.Reptilian species have been incorporated in comparative analyses of the vertebrate brain aimed at understanding the evolution of the sensory and cognitive novelties associated with the vertebrate central nervous system.
Other Transcriptomes
Stay tuned for additional transcriptomes from other reptilian species and/or specific organs.
Back to The LANE Web Site
Publications on Reptilian Transcriptomes
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✓Tzika A.C., Helaers R., Schramm G. & M. C. Milinkovitch
Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles
EvoDevo 2011, 2: 19
