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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 consensus sequences annotated with each reference species in the Ensembl or UniGene databases. The total number of consensuses is indicated in the middle of each graph.
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evv106-F6: Piecharts showing the percentage of consensus sequences annotated with each reference species in the Ensembl or UniGene databases. The total number of consensuses is indicated in the middle of each graph.

Mentions: In figure 6, we show the distribution of the consensus sequences named after an Ensembl or UniGene reference species gene. For all transcriptomes, most consensus sequences are named after the first reference species (used in the iterative BLAST searches) selected to be the most closely related to the species being annotated: Gallus is used for the annotation of 46% of the Al. mississippiensis sequences and Anolis is used for 46–74% of the sequences for the other reptilian species. For all the data sets, the combination of Anolis and Gallus sequences used as reference to build consensuses ranged from 56% to 87%. In all cases, there are more consensuses named after a Pelodiscus cDNA than after a Taeniopygia one, underlying the importance of using reference species from different taxonomic groups rather than several species from the same one. The remaining four non-Sauropsida species were used as reference to build only about 10% of the consensus sequences, due to their greater evolutionary distance.Fig. 6.—


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 consensus sequences annotated with each reference species in the Ensembl or UniGene databases. The total number of consensuses 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-F6: Piecharts showing the percentage of consensus sequences annotated with each reference species in the Ensembl or UniGene databases. The total number of consensuses is indicated in the middle of each graph.
Mentions: In figure 6, we show the distribution of the consensus sequences named after an Ensembl or UniGene reference species gene. For all transcriptomes, most consensus sequences are named after the first reference species (used in the iterative BLAST searches) selected to be the most closely related to the species being annotated: Gallus is used for the annotation of 46% of the Al. mississippiensis sequences and Anolis is used for 46–74% of the sequences for the other reptilian species. For all the data sets, the combination of Anolis and Gallus sequences used as reference to build consensuses ranged from 56% to 87%. In all cases, there are more consensuses named after a Pelodiscus cDNA than after a Taeniopygia one, underlying the importance of using reference species from different taxonomic groups rather than several species from the same one. The remaining four non-Sauropsida species were used as reference to build only about 10% of the consensus sequences, due to their greater evolutionary distance.Fig. 6.—

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