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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 contig/singletons annotated at each step of the pipeline. The number of input sequences for each transcriptome is indicated in the middle of each graph.
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evv106-F4: Piecharts showing the percentage of contig/singletons annotated at each step of the pipeline. The number of input sequences for each transcriptome is indicated in the middle of each graph.

Mentions: Our annotation pipeline (fig. 3 and supplementary fig. S1, Supplementary Material online) consists of iterative BLAST searches and identification of RBBH for a higher quality result, all steps being performed with the updated version of LANE runner (version 2.0). The filtered contigs and singletons of each reptilian transcriptome were compared with a BLASTn search to 1) the mitochondrial genome of the corresponding species or that of a closely related one and 2) a database including Ensembl v73 ncRNA sequences from eight reference species: A. carolinensis, Gallus gallus, Taeniopygia guttata, Pe. sinensis, Mus musculus, Homo sapiens, Xenopus tropicalis, and Danio rerio (hereafter named Anolis, Gallus, Taeniopygia, Pelodiscus Mus, Homo, Xenopus and Danio, to distinguish them as reference species from the annotated ones). Less than 1% of contigs and singletons corresponded to mtDNA sequences and only 1–4% to ncRNA (fig. 4). RBBH were identified with tBLASTx searches against the Ensembl v73 coding cDNA and “UniGene November 2013” databases of each reference species (fig. 3; see Supplementary Material online for details). Second, the sequences still nonannotated by this iterative process were aligned with tBLASTx against an “NCBI (National Center for Biotechnology Information) November 2013” database containing mRNA sequences from Sauropsida. The annotated sequences were divided into two data sets: 1) An annotation data set comprising all annotated sequences (with and without RBBH) and 2) a high quality phylogeny data set including only the annotated sequences with a RBBH. In a last round of BLAST searches, the nonannotated contigs/singletons of each reptilian species were compared with the annotation data set and the nonannotated sequences of the other seven reptilian transcriptomes. Finally, the remaining sequences were masked using RepeatMasker to check whether their lack of annotation was due to the presence of repetitive elements. The sequences lacking annotation after all these processes are called orphans (supplementary fig. S1, Supplementary Material online).Fig. 4.—


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 contig/singletons annotated at each step of the pipeline. The number of input sequences for each transcriptome 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-F4: Piecharts showing the percentage of contig/singletons annotated at each step of the pipeline. The number of input sequences for each transcriptome is indicated in the middle of each graph.
Mentions: Our annotation pipeline (fig. 3 and supplementary fig. S1, Supplementary Material online) consists of iterative BLAST searches and identification of RBBH for a higher quality result, all steps being performed with the updated version of LANE runner (version 2.0). The filtered contigs and singletons of each reptilian transcriptome were compared with a BLASTn search to 1) the mitochondrial genome of the corresponding species or that of a closely related one and 2) a database including Ensembl v73 ncRNA sequences from eight reference species: A. carolinensis, Gallus gallus, Taeniopygia guttata, Pe. sinensis, Mus musculus, Homo sapiens, Xenopus tropicalis, and Danio rerio (hereafter named Anolis, Gallus, Taeniopygia, Pelodiscus Mus, Homo, Xenopus and Danio, to distinguish them as reference species from the annotated ones). Less than 1% of contigs and singletons corresponded to mtDNA sequences and only 1–4% to ncRNA (fig. 4). RBBH were identified with tBLASTx searches against the Ensembl v73 coding cDNA and “UniGene November 2013” databases of each reference species (fig. 3; see Supplementary Material online for details). Second, the sequences still nonannotated by this iterative process were aligned with tBLASTx against an “NCBI (National Center for Biotechnology Information) November 2013” database containing mRNA sequences from Sauropsida. The annotated sequences were divided into two data sets: 1) An annotation data set comprising all annotated sequences (with and without RBBH) and 2) a high quality phylogeny data set including only the annotated sequences with a RBBH. In a last round of BLAST searches, the nonannotated contigs/singletons of each reptilian species were compared with the annotation data set and the nonannotated sequences of the other seven reptilian transcriptomes. Finally, the remaining sequences were masked using RepeatMasker to check whether their lack of annotation was due to the presence of repetitive elements. The sequences lacking annotation after all these processes are called orphans (supplementary fig. S1, Supplementary Material online).Fig. 4.—

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