Limits...
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.

Show MeSH

Related in: MedlinePlus

Assembly pipeline used to combine the “454” (in blue) and Illumina (in green) reads into nonredundant contigs (in red). Framed values correspond to those obtained for the E. macularius mix data set (multiple developmental stages and multiple adult organs), provided as an example. Dashed boxes delineate major steps of the assembly: (A) The “454” reads are de novo assembled, (B) the Illumina reads are aligned to the “454” assembly, and (C–E) iterative building of nonredundant Illumina contigs. The final assembly (F) includes both the “454” assembly and the Illumina contigs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4494049&req=5

evv106-F2: Assembly pipeline used to combine the “454” (in blue) and Illumina (in green) reads into nonredundant contigs (in red). Framed values correspond to those obtained for the E. macularius mix data set (multiple developmental stages and multiple adult organs), provided as an example. Dashed boxes delineate major steps of the assembly: (A) The “454” reads are de novo assembled, (B) the Illumina reads are aligned to the “454” assembly, and (C–E) iterative building of nonredundant Illumina contigs. The final assembly (F) includes both the “454” assembly and the Illumina contigs.

Mentions: We collected samples from individuals of our established Pa. guttatus and E. macularius colonies. Animal housing and samplings were performed in accordance with the Swiss animal welfare regulation (permit number 1008/3421/0). Normalized libraries (using the Trimmer-2 cDNA normalization kit; Evrogen) were prepared from 1) adult organs (testes, kidneys, and brain), and 2) embryos at two or three developmental stages (E10, E30, and E47 for Pa. guttatus and E8 and E24 for E. macularius). Each library was sequenced with the “454” (half-plate) and the Illumina (one lane, 100-base paired-end reads) technologies. For Pa. guttatus, we also included in the analyses our previously published vomeronasal organ (VNO) transcriptome (Brykczynska et al. 2013). We designed an assembly pipeline (incorporating SeqMan NGen v11.0; DNASTAR) presented in figure 2 to exclude redundancy among the “454” and Illumina contigs. Briefly, it comprises the following steps (detailed description in the supplementary methods, Supplementary Material online): 1) Assembly of the “454” reads (fig. 2A), 2) alignment of all the Illumina reads to the “454” assembly (fig. 2B), and 3) de novo and template assembly of the nonaligned Illumina reads (fig. 2C–E) in subsets of 40 million reads (due to computational resources limitation). The final assembly (fig. 2F) comprises the “454” assembly (contigs and singletons) and the Illumina contigs. Remaining adaptor sequences at the extremities or within contigs and singletons are removed with LANE runner. For each species, we assembled a mix of all cDNA libraries as well as each library (adults, embryos, or VNO) separately. To assess whether the mix assemblies are good representatives of the individual data sets, we compared the former with the latter by performing a template transcriptome assembly in NGen. Default parameters were used for template assemblies (with “other” as sequencing technology) except for the “Minimum Match Percentage” parameter that was set to 80. The mix assemblies were used for subsequent annotation. The “454” raw reads of the Al. mississippiensis brain transcriptome (Kunstner et al. 2010) were assembled with NGen, as well.Fig. 2.—


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)

Assembly pipeline used to combine the “454” (in blue) and Illumina (in green) reads into nonredundant contigs (in red). Framed values correspond to those obtained for the E. macularius mix data set (multiple developmental stages and multiple adult organs), provided as an example. Dashed boxes delineate major steps of the assembly: (A) The “454” reads are de novo assembled, (B) the Illumina reads are aligned to the “454” assembly, and (C–E) iterative building of nonredundant Illumina contigs. The final assembly (F) includes both the “454” assembly and the Illumina contigs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv106-F2: Assembly pipeline used to combine the “454” (in blue) and Illumina (in green) reads into nonredundant contigs (in red). Framed values correspond to those obtained for the E. macularius mix data set (multiple developmental stages and multiple adult organs), provided as an example. Dashed boxes delineate major steps of the assembly: (A) The “454” reads are de novo assembled, (B) the Illumina reads are aligned to the “454” assembly, and (C–E) iterative building of nonredundant Illumina contigs. The final assembly (F) includes both the “454” assembly and the Illumina contigs.
Mentions: We collected samples from individuals of our established Pa. guttatus and E. macularius colonies. Animal housing and samplings were performed in accordance with the Swiss animal welfare regulation (permit number 1008/3421/0). Normalized libraries (using the Trimmer-2 cDNA normalization kit; Evrogen) were prepared from 1) adult organs (testes, kidneys, and brain), and 2) embryos at two or three developmental stages (E10, E30, and E47 for Pa. guttatus and E8 and E24 for E. macularius). Each library was sequenced with the “454” (half-plate) and the Illumina (one lane, 100-base paired-end reads) technologies. For Pa. guttatus, we also included in the analyses our previously published vomeronasal organ (VNO) transcriptome (Brykczynska et al. 2013). We designed an assembly pipeline (incorporating SeqMan NGen v11.0; DNASTAR) presented in figure 2 to exclude redundancy among the “454” and Illumina contigs. Briefly, it comprises the following steps (detailed description in the supplementary methods, Supplementary Material online): 1) Assembly of the “454” reads (fig. 2A), 2) alignment of all the Illumina reads to the “454” assembly (fig. 2B), and 3) de novo and template assembly of the nonaligned Illumina reads (fig. 2C–E) in subsets of 40 million reads (due to computational resources limitation). The final assembly (fig. 2F) comprises the “454” assembly (contigs and singletons) and the Illumina contigs. Remaining adaptor sequences at the extremities or within contigs and singletons are removed with LANE runner. For each species, we assembled a mix of all cDNA libraries as well as each library (adults, embryos, or VNO) separately. To assess whether the mix assemblies are good representatives of the individual data sets, we compared the former with the latter by performing a template transcriptome assembly in NGen. Default parameters were used for template assemblies (with “other” as sequencing technology) except for the “Minimum Match Percentage” parameter that was set to 80. The mix assemblies were used for subsequent annotation. The “454” raw reads of the Al. mississippiensis brain transcriptome (Kunstner et al. 2010) were assembled with NGen, as well.Fig. 2.—

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