Supporting data for "Improving amphibian genomic resources: a multi-tissue reference transcriptome of an iconic invader"

Dataset type: Genomic, Transcriptomic
Data released on November 13, 2017

Richardson MF; Sequeira F; Selechnik D; Carneiro M; Vallinoto M; Reid JG; West AJ; Crossland MR; Shine R; Rollins LA (2017): Supporting data for "Improving amphibian genomic resources: a multi-tissue reference transcriptome of an iconic invader" GigaScience Database. http://dx.doi.org/10.5524/100374

DOI10.5524/100374

Cane toads (Rhinella marina) are an iconic invasive species introduced to four continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range. Using approximately 1.9 billion reads, from developing tadpoles and 6 adult tissue-specific cDNA libraries, and a transcriptome assembly pipeline encompassing 100 separate de novo assemblies, we constructed 62,202 transcripts, of which we functionally annotated ~50 %. Our transcriptome assembly exhibits 90% full-length completeness of the BUSCO (benchmarking universal single-copy orthologs) dataset. Robust assembly metrics and comparisons to several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. This comprehensive anuran transcriptome will provide a valuable resource for investigation of genes under selection during invasion in cane toads, but will also greatly expand our general knowledge of anuran genomes, which are underrepresented in the literature. The dataset is publically available in NCBI and GigaDB to serve as a resource for other researchers.

Additional details

Read the peer-reviewed publication(s):

Richardson, M. F., Sequeira, F., Selechnik, D., Carneiro, M., Vallinoto, M., Reid, J. G., … Rollins, L. A. (2017). Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader. GigaScience, 7(1). doi:10.1093/gigascience/gix114

Related datasets:

doi:10.5524/100374 IsPartOf doi:10.5524/100483

Additional information:

http://www.xenbase.org/other/static/ftpDatafiles.jsp

Accessions (data included in GigaDB):

Bioproject: PRJNA383966
Bioproject: PRJNA382870

Accessions (data not in GigaDB):

Bioproject: PRJNA277985
Bioproject: PRJNA255079





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RMTP8386cane toadmarine toadRhinella marina Description:RNA from liver of Cane Toad, RMTP
Alternative names:cane toad
Alternative accession-BioSample:SAMN2910015
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S18386cane toadmarine toadRhinella marina Description:RNA from spleen of Cane Toad, S1
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756319
...
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S188386cane toadmarine toadRhinella marina Description:RNA from spleen of Cane Toad, S18
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756321
...
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S198386cane toadmarine toadRhinella marina Description:RNA from spleen of Cane Toad, S19
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756322
...
+
S28386cane toadmarine toadRhinella marina Description:RNA from spleen of Cane Toad, S2
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756320
...
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T18386cane toadmarine toadRhinella marina Description:RNA from Cane Toad (tadpole, whole org...
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756323
...
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T108386cane toadmarine toadRhinella marina Description:RNA from Cane Toad (tadpole, whole org...
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756326
...
+
T48386cane toadmarine toadRhinella marina Description:RNA from Cane Toad (tadpole, whole org...
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756324
...
+
T78386cane toadmarine toadRhinella marina Description:RNA from Cane Toad (tadpole, whole org...
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756325
...
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Displaying 11-19 of 19 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
sequence assemblyFASTA4.8 GB2017-11-06
Transcriptome sequenceFASTA12.07 GB2017-11-06
otherTEXT251.45 KB2017-11-01
Transcriptome sequenceFASTA127.22 MB2017-11-06
otherUNKNOWN46.17 MB2017-11-06
ReadmeTEXT4.26 KB2017-11-01
annotationTEXT44.71 MB2017-11-01
annotationTEXT20.75 MB2017-11-01
protein sequenceFASTA58.36 MB2017-11-01
sequence assemblyFASTA81.17 MB2017-11-06
Displaying 1-10 of 12 File(s).
Funding body Awardee Award ID Comments
Australian Research Council R Shine FL120100074
Australian Research Council LA Rollins DE150101393
Date Action
November 13, 2017 Dataset publish
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix114