Data from: Rapid molecular evolution across amniotes of the IIS/TOR network

McGaugh SE, Bronikowski AM, Kuo C, Reding DM, Addis EA, Flagel LE, Janzen FJ, Schwartz TS

Date Published: May 21, 2015

DOI: http://dx.doi.org/10.5061/dryad.vn872

 

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Title TRANSCRIPTOMES.tar
Downloaded 16 times
Description TRANSCRIPTOMES folder includes: (1) The transcriptome assembly for each of the 18 reptile individuals sequenced (e.g. file name: SM1_centroids_nucleotides.fasta), see list below. These contain the longest open reading frames (ORFs) produced by Trinity, which were then clustered by UCLUST into centroids to reduce redundancy within a single species' transcriptome. A centroid may have collapsed multiple isoforms, truncated transcripts, and alleles from a gene, but it may also have collapsed very recent paralogs. Files are named by sequence identifier (e.g. SM) listed below. (2) The Trinotate annotation databases for each transcriptome (e.g. file name: trinotate_annotation_report_SM1.xls). The prot_id corresponds to the centroid sequence in the transcriptome .fasta file. (3) An ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta files). OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analysed for the paper). Sequence ID, Common Name, Species ID SM1, Snapping turtle, Cheyldra serpentina SM2, Anolis lizard, Anolis sagrei SM3, California alligator lizard, Elgaria multicarinata SM4, African House, Lamprophis fuliginosus SM5, Cottonmouth, Agkistrodon piscivorus SM6, Sunbeam snake, Xenopeltis unicolor SM7, Alligator, Alligator mississippiensis SM8, Fence Lizard, Sceloporus undulatus SM9, Bearded dragon, Pogona vitticeps SM10, Stinkpot turtle, Sternotherus odoratus SM11, Sideneck turtle, Pelusios castaneus SM12, Skink, Scincella lateralis SM13, Box turtle, Terrapene ornata SM14, Viper Boa, Candoia aspera SM15, Gecko, Eublepharis macularius TC, Western aquatic garter snake, Thamnophis couchii HS08, Western terrestrial garter snake –lakeshore (fast-living) ecotype, Thamnophis elegans HS11, Western terrestrial garter snake –meadow (slow-living) ecotype, Thamnophis elegans
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Title ALIGNED_BEST_FIRST_1500_ORTHOLOGS.tar
Downloaded 26 times
Description ALIGNED_BEST_FIRST_15000_ORTHOLOGS folder: “Best” ortholog amino acid and nucleotide alignments. The 104,235 putative orthologs described in ALIGNED_ALL-ORTHOLOGS often contained more than two representative sequences per species. For the first 15,000 putative orthologs (those with the most species included in the alignments) we used UCLUST to find the best representative per species per ortholog by taking the sequence that was closest to the centroid for that ortholog. Alignments contain one representative per species per alignment (found by centroid clustering explained in the methods) are given for Orthologs 1-15,000, regardless of how many species are contained in the centroid. After designating one representative sequence per species, alignments were performed as described in the methods (e.g. MSAProbs followed by TranslatorX). Amino acid and nucleotides are given in their respective folders. - Also included in each folder is an ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file). OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).
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Title ALIGNED_ALL_ORTHOLOGS.tar
Downloaded 2 times
Description ALIGNED_ALL_ORTHOLOGS folder: We used OrthoMCL to cluster ORF-centroids from all species into putative orthologs from all the species included in this study. This folder contains the putative ortholog amino acid alignments and corresponding nucleotide alignments for which there were two or more species present in the ortholog clustered by OrthoMCL (104,235 total alignments). These are available as separate files for each ortholog (104,235 total orthologs with two or more species). Amino acid and nucleotides are given in their respective folders. - Also included is an ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file). OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).
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Title IIS-TOR_TEST_GENES.tar
Downloaded 6 times
Description IIS-TOR_TEST_GENES folder: The hand-curated nucleotide and amino acid alignments for 61 IIS/TOR network genes. The supplementary text in the PNAS paper explains the quality controls. These were the final alignments used in the PAML and Ka/Ks analyses. This folder also contains an excel file with the annotation for the IIS/TOR test genes.
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Title Species.Identifier
Downloaded 29 times
Description Species.Identifiers file. For the species included in this study this file contains the (i) Sequence Identifier (for the transcriptomes we developed) or the Ensemble identifier (for the genomes and transcriptomes we downloaded); (2) the species name; (3) the common name; (4) any "nicknames" that were used during the analysis, and (5) the identifiers used in the alignments. Further details on these individuals used in this study can be found in Supplementary Table 2 of the PNAS paper (McGaugh et al. 2015 PNAS).
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Title Ortholog_Key
Downloaded 8 times
Description An ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file). OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).
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Title CONTROL_GENES.tar
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Description CONTROL_GENES folder: The final nucleotide and amino acid alignments for the 1417 "control genes". This folder also contains an excel file with the annotation for the control genes.
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Title Readme
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Description The Readme file explaining the contents of this Dryad submission.
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When using this data, please cite the original publication:

McGaugh SE, Bronikowski AM, Kuo C, Reding DM, Addis EA, Flagel LE, Janzen FJ, Schwartz TS (2015) Data from: Rapid molecular evolution across amniotes of the IIS/TOR network. Proceedings of the National Academy of Sciences of the United States of America 112(22): 7055-7060. http://dx.doi.org/10.1073/pnas.1419659112

Additionally, please cite the Dryad data package:

McGaugh SE, Bronikowski AM, Kuo C, Reding DM, Addis EA, Flagel LE, Janzen FJ, Schwartz TS (2015) Data from: Rapid molecular evolution across amniotes of the IIS/TOR network. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vn872
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