Reptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation.
Researchers have used 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species:
- Nile Crocodile
- Corn Snake
- Bearded Dragon
- Red-eared Turtle
Using an in-house pipeline for recursive similarity searches of >3,000,000 reads against multiple databases from 7 reference vertebrates, they compile a reptilian comparative transcriptomics dataset, with homology assignment for 20,000 to 31,000 transcripts per species and a cumulated non-redundant sequence length of 248.6 Mbases. This approach identifies the majority (87%) of chicken brain transcripts and about 50% of de novo assembled reptilian transcripts.
In addition to 57,502 microsatellite loci, they identify thousands of SNP and indel polymorphisms for population genetic and linkage analyses. The researchers also build very large multiple alignments for Sauropsida and mammals (2 millions residues per species) and perform extensive phylogenetic analyses suggesting that turtles are not basal living reptiles but are rather associated with Archosaurians, hence, potentially answering a long-standing question in the phylogeny of Amniotes.
The reptilian transcriptome should prove a useful new resource as reptiles are becoming important new models for comparative genomics, ecology, and evolutionary developmental genetics.
The Reptilian Transcriptome data is freely available at http://www.reptilian-transcriptomes.org/
- Tzika AC, Helaers R, Schramm G, Milinkovitch MC. (2011) Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles EvoDevo [Epub ahead of print]. [abstract]