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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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Outline of the transcriptome annotation pipeline. All steps included in the outer dash-framed box are performed in LANE runner. The steps of a single iteration (i.e., using one reference species) are grouped in the inner dashed frame. The reference species iteratively considered for annotation are listed in the inset. Query sequences having a hit are indicated with a yellow mark and those having an RBBH with a green mark.
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evv106-F3: Outline of the transcriptome annotation pipeline. All steps included in the outer dash-framed box are performed in LANE runner. The steps of a single iteration (i.e., using one reference species) are grouped in the inner dashed frame. The reference species iteratively considered for annotation are listed in the inset. Query sequences having a hit are indicated with a yellow mark and those having an RBBH with a green mark.

Mentions: We annotated the transcriptomes and/or genomes of the following representatives of the four extant reptilian orders: 1) Six Squamata, including three snakes (P. molurus, Pa. guttatus, and T. elegans) and three lizards (E. macularius, Cham. chamaeleon, and C. ocellatus); 2) three Crocodilia (G. gangeticus, Cr. porosus, and Al. mississippiensis); 3) the single living Rhynchocephalia (S. punctatus); and 4) one Testudines (Chr. picta). Table 1 contains detailed information on the data sets and figure 1 shows the phylogenetic relationships among these species together with the reference species used for annotation (topology and divergence times based on the “Timetree of Life” estimates; Hedges et al. 2006). During our study, additional reptilian transcriptomes and genomes became available (e.g., Margres et al. 2013; Vonk et al. 2013; Wang et al. 2013); however, they either correspond to species closely related to the ones already selected or the transcriptomes originate from very specialized organs (e.g., the venom glands of snakes), in which case there is a high abundance of tissue-specific transcripts (e.g., coding for venom toxins) rather than a wide coverage of the species’ transcriptome. Similarly to the Reptilian Transcriptome 1.0 (Tzika et al. 2011), the annotation in the Reptilian Transcriptomes 2.0 is based on iterative BLAST searches, but with three major modifications: 1) The identification of RBBH to obtain a higher quality annotation (Altenhoff and Dessimoz 2009; Dalquen and Dessimoz 2013); 2) the use of the improved BLAST+ (release 2.2.28; Camacho et al. 2009), instead of the wwwblast web server; and 3) the use of Clustal Omega, instead of MUSCLE, as the multiple sequence alignment software for consensus building. The software LANE runner (Tzika et al. 2011) was upgraded (version 2.0) to accommodate these modifications. An overview of the annotation pipeline is presented in figure 3 and supplementary figure S1, Supplementary Material online, and a detailed description of the process is given in the supplementary methods and figure S2, Supplementary Material online.Fig. 3.—


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)

Outline of the transcriptome annotation pipeline. All steps included in the outer dash-framed box are performed in LANE runner. The steps of a single iteration (i.e., using one reference species) are grouped in the inner dashed frame. The reference species iteratively considered for annotation are listed in the inset. Query sequences having a hit are indicated with a yellow mark and those having an RBBH with a green mark.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv106-F3: Outline of the transcriptome annotation pipeline. All steps included in the outer dash-framed box are performed in LANE runner. The steps of a single iteration (i.e., using one reference species) are grouped in the inner dashed frame. The reference species iteratively considered for annotation are listed in the inset. Query sequences having a hit are indicated with a yellow mark and those having an RBBH with a green mark.
Mentions: We annotated the transcriptomes and/or genomes of the following representatives of the four extant reptilian orders: 1) Six Squamata, including three snakes (P. molurus, Pa. guttatus, and T. elegans) and three lizards (E. macularius, Cham. chamaeleon, and C. ocellatus); 2) three Crocodilia (G. gangeticus, Cr. porosus, and Al. mississippiensis); 3) the single living Rhynchocephalia (S. punctatus); and 4) one Testudines (Chr. picta). Table 1 contains detailed information on the data sets and figure 1 shows the phylogenetic relationships among these species together with the reference species used for annotation (topology and divergence times based on the “Timetree of Life” estimates; Hedges et al. 2006). During our study, additional reptilian transcriptomes and genomes became available (e.g., Margres et al. 2013; Vonk et al. 2013; Wang et al. 2013); however, they either correspond to species closely related to the ones already selected or the transcriptomes originate from very specialized organs (e.g., the venom glands of snakes), in which case there is a high abundance of tissue-specific transcripts (e.g., coding for venom toxins) rather than a wide coverage of the species’ transcriptome. Similarly to the Reptilian Transcriptome 1.0 (Tzika et al. 2011), the annotation in the Reptilian Transcriptomes 2.0 is based on iterative BLAST searches, but with three major modifications: 1) The identification of RBBH to obtain a higher quality annotation (Altenhoff and Dessimoz 2009; Dalquen and Dessimoz 2013); 2) the use of the improved BLAST+ (release 2.2.28; Camacho et al. 2009), instead of the wwwblast web server; and 3) the use of Clustal Omega, instead of MUSCLE, as the multiple sequence alignment software for consensus building. The software LANE runner (Tzika et al. 2011) was upgraded (version 2.0) to accommodate these modifications. An overview of the annotation pipeline is presented in figure 3 and supplementary figure S1, Supplementary Material online, and a detailed description of the process is given in the supplementary methods and figure S2, Supplementary Material online.Fig. 3.—

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