Data from: Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq

Marra NJ, Romero A, DeWoody JA

Date Published: April 18, 2014

DOI: http://dx.doi.org/10.5061/dryad.ts98d

 

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Title Blast Descriptions for contigs from Dipodomys spectabilis kidney transcriptome assembly
Downloaded 43 times
Description These are the preliminary blast descriptions for contigs from the combined assembly of 454 and Illumina reads pooled from 4 individual Dipodomys spectabilis kidney libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e<1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 35 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).
Download D_spectabilis_blastdatafinalall.txt (3.722 Mb)
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Title Blast Descriptions for contigs from Heteromys desmarestianus kidney transcriptome assembly
Downloaded 56 times
Description These are the preliminary blast descriptions for contigs from the combined assembly of 454 and Illumina reads pooled from 4 individual Heteromys desmarestianus kidney libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e<1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 25 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).
Download H_desm_kidney_blast_descriptions.txt (3.569 Mb)
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Title D_spectabilis_kidney_transcriptome
Downloaded 24 times
Description Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
Download D_spectabilis_kidney_transcriptome.fasta (45.28 Mb)
Download README.txt (1.184 Kb)
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Title Blast Descriptions for contigs from Chaetodipus baileyi kidney transcriptome assembly
Downloaded 31 times
Description These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads pooled from 4 individual Chaetodipus baileyi kidney libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e<1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 25 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).
Download C_bail_blast_descriptions.txt (3.466 Mb)
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Title C_baileyi_kidney_transcriptome
Downloaded 9 times
Description Transcriptome assembly from combined assembly Illumina reads. These reads were assembled first in Trinity and then fragmented and assembled in gsAssembler (see methods of manuscript for more details and rationale)
Download C_baileyi_kidney_transcriptome.fasta (50.93 Mb)
Download README.txt (1.155 Kb)
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Title H_desmarestianus_transcriptome
Downloaded 14 times
Description Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
Download H_desmarestianus_transcriptome.fasta (46.40 Mb)
Download README.txt (1.187 Kb)
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Title Guide Tree for PAML analysis
Downloaded 11 times
Description This is the tree that was used in codeml as a guide tree for the branch and branch-site tests (see text of methods). The tree is unrooted to as is required for these tests. The two desert lineages, Dipodomys spectabilis and Chaetodipus baileyi have been marked with #1 to indicate them as foreground branches to be assigned a different rate than the rest of the tree. D_spec = Dipodomys spectabilis, C_bail = Chaetodipus baileyi, H_desm = Heteromys desmarestianus, M_musc = Mus musculus.
Download COI_tree_unrooted_marked.newick (40 bytes)
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When using this data, please cite the original publication:

Marra NJ, Romero A, DeWoody JA (2014) Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq. Molecular Ecology 23(11): 2699-2711. http://dx.doi.org/10.1111/mec.12764

Additionally, please cite the Dryad data package:

Marra NJ, Romero A, DeWoody JA (2014) Data from: Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ts98d
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