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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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Piecharts showing the percentage of nonannotated contigs/singletons that match with the other annotated reptilian transcriptomes. The total number of hits is indicated in the middle of each graph.
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evv106-F5: Piecharts showing the percentage of nonannotated contigs/singletons that match with the other annotated reptilian transcriptomes. The total number of hits is indicated in the middle of each graph.

Mentions: The BLAST searches among the reptilian transcriptomes substantially improved the snakes’ annotation (figs. 4 and 5), as 7 to 10% of their contigs/singletons matched with other transcriptomes, mainly those of other snakes. In particular, 93% of the T. elegans sequences still nonannotated after BLAST searches against Ensembl, UniGene and NCBI Sauropsida mRNAs, matched a Pa. guttatus sequence (fig. 5). Similar results are obtained for the reverse comparison (87% of the nonannotated Pa. guttatus sequences matched T. elegans). These results strongly suggest that these sequences represent snake-specific transcripts. For the other transcriptomes, only a small number (<1,200) of contigs/singletons were annotated, probably because none of these reptiles is more closely related to each others than to one of the Archosauria or Squamata reference species (Anolis and Gallus) (fig. 1). Finally, very few repetitive elements were identified, with the highest percentage of masked sequences in Al. mississippiensis (4%) and ≤1% for all the other species.Fig. 5.—


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)

Piecharts showing the percentage of nonannotated contigs/singletons that match with the other annotated reptilian transcriptomes. The total number of hits is indicated in the middle of each graph.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv106-F5: Piecharts showing the percentage of nonannotated contigs/singletons that match with the other annotated reptilian transcriptomes. The total number of hits is indicated in the middle of each graph.
Mentions: The BLAST searches among the reptilian transcriptomes substantially improved the snakes’ annotation (figs. 4 and 5), as 7 to 10% of their contigs/singletons matched with other transcriptomes, mainly those of other snakes. In particular, 93% of the T. elegans sequences still nonannotated after BLAST searches against Ensembl, UniGene and NCBI Sauropsida mRNAs, matched a Pa. guttatus sequence (fig. 5). Similar results are obtained for the reverse comparison (87% of the nonannotated Pa. guttatus sequences matched T. elegans). These results strongly suggest that these sequences represent snake-specific transcripts. For the other transcriptomes, only a small number (<1,200) of contigs/singletons were annotated, probably because none of these reptiles is more closely related to each others than to one of the Archosauria or Squamata reference species (Anolis and Gallus) (fig. 1). Finally, very few repetitive elements were identified, with the highest percentage of masked sequences in Al. mississippiensis (4%) and ≤1% for all the other species.Fig. 5.—

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.

Show MeSH
Related in: MedlinePlus