Reptilian transcriptomes v2

The second version of the Reptilian transcriptomes database provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages.

Reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the ‘Reptilian Transcriptomes Database 2.0’ which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively.

The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles.

Associated Publication
Tzika A.C., Ullate-Agote A., Grbic D. & M. C. Milinkovitch
Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics
Genome Biol. Evol. 7: 1827-1841 (2015)
Supplementary Materials

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You can perform BLAST searches against all the datasets using our WWWBLAST server.

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All files are compressed (zipped) FASTA files.