Reptilian-Transcriptomes v2.0

This database provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. This resource should prove useful for the genomic/transcriptomic and herpetology communities alike, as reptiles are still largely under-represented in genome and transcriptome databases (despite that they include twice as many species as mammals) and are becoming important new models for comparative genomics, ecology, and evolutionary developmental genetics. The major lineages of Reptilia diverged 200-280 million years ago and include more than 10,000 species which display a remarkable range of life histories, sex-determining systems, reproductive modes, physiologies, and body plans.

Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, 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 (Tzika et al. 2011, 2015).

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.

The ‘Reptilian-transcriptomes.org’ database, website and wwwblast server are hosted in the Laboratory of Artificial & Natural Evolution (LANE) at the University of Geneva (Switzerland) and the project is funded by the Swiss National Science Foundation and the SIB Swiss Institute of Bioinformatics.

1. ➡Search the Database 2.0 through our WWWBLAST local server
   

2. ➡Download all Reptilian Transcriptomes v2.0 data (contigs and consensus sequences)
   

3. ➡Download here LANE runner v2.0, a JAVA application (& user manual) with a user-friendly interface that integrates:
   

1. 1.Iterative BLAST+ searches (Camacho et al. 2009) against multiple databases,
   

2. 2.Reciprocal Best BLAST Hits (RBBH) identification for homology assessment, and
   

3. 3.Consensus sequence building to assemble sequences exhibiting the same annotation.
   

Publication

1. ✓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)
   

2. Open Access
   

3. Download the Supplementary Materials file
   

4. Database website: Reptilian-Transcriptomes v2.0
   

Related publications

1. ✓Ullate-Agote A., Milinkovitch M.C. & A.C. Tzika
   The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates
   Int. J. Dev. Biol. 58: 881-888 (2014)
   

2. Open Access
   

3. ✓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
   

4. Open Access
   

5. Database website: Reptilian-Transcriptomes v1.0 (brain transcriptomes)
   

6. ✓Brykczynska U., Tzika A.C., Rodriguez I. & M. C. Milinkovitch
   Contrasted evolution of the vomeronasal receptor repertoires in Mammals and Squamate reptiles
   Genome Biology & Evolution 5: 389-401 (2013)
   

7. Open Access
   

8. Download the Supplementary Materials file
   

9. VNO Transcriptome
   

10. ✓Tzika A. C. & M. C. Milinkovitch.
    A Pragmatic Approach for Selecting Evo-Devo Model Species in Amniotes
    Chapter 7 Pages 119-140 in ‘Evolving Pathways; Key Themes in Evolutionary Developmental Biology’ (A. Minelli & G. Fusco, eds.), Cambridge University Press 2008
    

11. e-mail
    

1. ✓Milinkovitch M.C. & A. C. Tzika
   Escaping the Mouse Trap; the Selection of New Evo-Devo Model Species
   Journal of Experimental Zoology (Mol. Dev. Evol.) 308B: 337–346 (2007)
   

2. e-mail
   

3. News Coverage
   

Previous version of the Reptilian Transcriptomes database

Database v1.0: Brain Transcriptomes

The first version of Reptilian-Transcriptomes.org focused on brain transcriptomes from four reptilian and one avian species: the Nile crocodile, the Corn snake, the Bearded dragon, the red-eared turtle as well as the chicken (Gallus gallus) as a reference species.
The Reptilian-Transcriptomes v2.0 (see above) is largely more complete than v1.0 as it provides extensive annotation of transcriptomes from multiple organs and multiple developmental stages, as well as of genomes, from 17 reptilian species. Also, the LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show (see Tzika et al. Genome Biol. Evol. 2015; full reference above) that this approach substantially increases the annotation completeness of the assembled transcriptomes/genomes.

VNO Transcriptome

The vomeronasal organ (VNO) is an olfactory structure that detects pheromones and environmental cues. It has been suggested that the shift in habitat of early tetrapods from water to land is reflected by an increase in the ratio of V1R/V2R genes. Snakes, that have a very large VNO associated with a sophisticated tongue delivery system, were missing from this analysis. We used RNA-seq and RNA in-situ hybridization to study the  diversity, evolution, and expression pattern of the corn snake vomeronasal receptor repertoires. Our analyses indicate that snakes and lizards retain an extremely limited number of V1R genes but exhibit a large number of V2R genes, including multiple lineages of reptile-specific and snake-specific expansions. We also showed that the peculiar bigenic pattern of V2R vomeronasal receptor gene transcription observed in mammals is conserved in squamate reptiles, hinting at an important but unknown functional role played by this expression strategy. Our results do not support the hypothesis that the shift to a vomeronasal receptor repertoire dominated by V1Rs in mammals reflects the evolutionary transition of early tetrapods from water to land. This study shed light on the evolutionary dynamics of the vomeronasal receptor families in vertebrates and reveals how mammals and squamates differentially adapted the same ancestral vomeronasal repertoire to succeed in a terrestrial environment. More information is available here.