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Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Tzika AC, Ullate-Agote A, Grbic D, Milinkovitch MC - Genome Biol Evol (2015)

Bottom Line: 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.The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland athanasia.tzika@unige.ch michel.milinkovitch@unige.ch.

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Chronogram among the selected reptilian and reference species used for annotation. The letters between parentheses after the species names indicate the data type (T, transcriptome; G, genome; GR, genome of a reference species). The underlined species were newly sequenced in our laboratory for this study. The tree topology and divergence times are based on the “TimeTree of Life” estimates (Hedges et al. 2006).
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evv106-F1: Chronogram among the selected reptilian and reference species used for annotation. The letters between parentheses after the species names indicate the data type (T, transcriptome; G, genome; GR, genome of a reference species). The underlined species were newly sequenced in our laboratory for this study. The tree topology and divergence times are based on the “TimeTree of Life” estimates (Hedges et al. 2006).

Mentions: The aim of this study is to build the second version of the “Reptilian Transcriptomes Database” (http://www.reptilian-transcriptomes.org, last accessed June 10, 2015; Tzika et al. 2011), providing a high-quality and extensive annotation of transcriptomes and genomes from species that cover the major lineages of the Class Reptilia. We generated new transcriptomic data from two species, of interest for evolutionary developmental studies: The leopard gecko, Eublepharis macularius, and the corn snake, Pa. guttatus. For both species, Roche 454 and Illumina reads were sequenced from normalized cDNA libraries of multiple adult tissues (brain, kidneys, testes) and various embryonic stages. We also gathered published reptilian transcriptomic/genomic data sets, selecting representatives of the four extant orders (fig. 1): 1) Four Squamata, including two snakes (P. molurus [Castoe et al. 2011] and Thamnophis elegans [Schwartz et al. 2010]) and two lizards (Chalcides ocellatus [Brandley et al. 2012] and Chamaeleo chamaeleon [Bar-Yaacov et al. 2013]); 2) the single living tuatara species, Sphenodon punctatus (Miller et al. 2012); 3) three Crocodilia species (Cr. porosus [St John et al. 2012], Al. mississippiensis [Kunstner et al. 2010], and G. gangeticus); and 4) one Testudines (Chr. picta [Shaffer et al. 2013]).Fig. 1.—


Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Tzika AC, Ullate-Agote A, Grbic D, Milinkovitch MC - Genome Biol Evol (2015)

Chronogram among the selected reptilian and reference species used for annotation. The letters between parentheses after the species names indicate the data type (T, transcriptome; G, genome; GR, genome of a reference species). The underlined species were newly sequenced in our laboratory for this study. The tree topology and divergence times are based on the “TimeTree of Life” estimates (Hedges et al. 2006).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494049&req=5

evv106-F1: Chronogram among the selected reptilian and reference species used for annotation. The letters between parentheses after the species names indicate the data type (T, transcriptome; G, genome; GR, genome of a reference species). The underlined species were newly sequenced in our laboratory for this study. The tree topology and divergence times are based on the “TimeTree of Life” estimates (Hedges et al. 2006).
Mentions: The aim of this study is to build the second version of the “Reptilian Transcriptomes Database” (http://www.reptilian-transcriptomes.org, last accessed June 10, 2015; Tzika et al. 2011), providing a high-quality and extensive annotation of transcriptomes and genomes from species that cover the major lineages of the Class Reptilia. We generated new transcriptomic data from two species, of interest for evolutionary developmental studies: The leopard gecko, Eublepharis macularius, and the corn snake, Pa. guttatus. For both species, Roche 454 and Illumina reads were sequenced from normalized cDNA libraries of multiple adult tissues (brain, kidneys, testes) and various embryonic stages. We also gathered published reptilian transcriptomic/genomic data sets, selecting representatives of the four extant orders (fig. 1): 1) Four Squamata, including two snakes (P. molurus [Castoe et al. 2011] and Thamnophis elegans [Schwartz et al. 2010]) and two lizards (Chalcides ocellatus [Brandley et al. 2012] and Chamaeleo chamaeleon [Bar-Yaacov et al. 2013]); 2) the single living tuatara species, Sphenodon punctatus (Miller et al. 2012); 3) three Crocodilia species (Cr. porosus [St John et al. 2012], Al. mississippiensis [Kunstner et al. 2010], and G. gangeticus); and 4) one Testudines (Chr. picta [Shaffer et al. 2013]).Fig. 1.—

Bottom Line: 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.The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Switzerland SIB Swiss Institute of Bioinformatics, Switzerland Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Switzerland athanasia.tzika@unige.ch michel.milinkovitch@unige.ch.

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Related in: MedlinePlus