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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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Completeness of the annotated transcriptomes assessed with four reference data sets: Ramskold ubiquitously expressed genes in human (blue bars), CEGMA core human genes (red bars), OrthoDB7 BUSCOs from the vertebrate (green bars), and the metazoan (purple bars) radiation nodes. The species are ordered from higher to lower overlap with the Ramskold data set and Anolis is shown as reference.
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evv106-F7: Completeness of the annotated transcriptomes assessed with four reference data sets: Ramskold ubiquitously expressed genes in human (blue bars), CEGMA core human genes (red bars), OrthoDB7 BUSCOs from the vertebrate (green bars), and the metazoan (purple bars) radiation nodes. The species are ordered from higher to lower overlap with the Ramskold data set and Anolis is shown as reference.

Mentions: We verified the quality of our annotations by assessing their completeness against four established data sets (fig. 7): A set of ubiquitously expressed genes in human tissues and cell lines (Ramskold et al. 2009), a selection of eukaryotic genes from the CEGMA (Parra et al. 2007), and two “Benchmarking sets of Universal Single-Copy Orthologs” (BUSCOs; from OrthoDB7 [Waterhouse et al. 2013]) in Vertebrata and Metazoa. The comparisons were performed by BLASTn searches of the reference data sets against the consensuses of the phylogeny data sets. In the case of Al. mississippiensis, the results of the transcriptome and genome annotations were combined.Fig. 7.—


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)

Completeness of the annotated transcriptomes assessed with four reference data sets: Ramskold ubiquitously expressed genes in human (blue bars), CEGMA core human genes (red bars), OrthoDB7 BUSCOs from the vertebrate (green bars), and the metazoan (purple bars) radiation nodes. The species are ordered from higher to lower overlap with the Ramskold data set and Anolis is shown as reference.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv106-F7: Completeness of the annotated transcriptomes assessed with four reference data sets: Ramskold ubiquitously expressed genes in human (blue bars), CEGMA core human genes (red bars), OrthoDB7 BUSCOs from the vertebrate (green bars), and the metazoan (purple bars) radiation nodes. The species are ordered from higher to lower overlap with the Ramskold data set and Anolis is shown as reference.
Mentions: We verified the quality of our annotations by assessing their completeness against four established data sets (fig. 7): A set of ubiquitously expressed genes in human tissues and cell lines (Ramskold et al. 2009), a selection of eukaryotic genes from the CEGMA (Parra et al. 2007), and two “Benchmarking sets of Universal Single-Copy Orthologs” (BUSCOs; from OrthoDB7 [Waterhouse et al. 2013]) in Vertebrata and Metazoa. The comparisons were performed by BLASTn searches of the reference data sets against the consensuses of the phylogeny data sets. In the case of Al. mississippiensis, the results of the transcriptome and genome annotations were combined.Fig. 7.—

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