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Data released on November 13, 2017

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

Richardson, M, F; Sequeira, F; Selechnik, D; Carneiro, M; Vallinoto, M; Reid, J, G; West, A, J; Crossland, M, R; Shine, R; Rollins, L, A (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 RIS BibTeX Text

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.

Contact Submitter

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

Keywords:

de novo assembly bufo marinus cane toad rhinella marina invasive species rna-seq transcriptome anuran amphibian 

Genomic, Transcriptomic

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Funding:

  • Funding body - Australian Research Council
  • Award ID - FL120100074
  • Awardee - R Shine
  • Funding body - Australian Research Council
  • Award ID - DE150101393
  • Awardee - LA Rollins

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
AR058386cane toadmarine toadRhinella marina Description:RNA from testes of Cane Toad, AR05
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756328
...
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AR198386cane toadmarine toadRhinella marina Description:RNA from ovary of Cane Toad, AR19
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756327
...
+
B198386cane toadmarine toadRhinella marina Description:RNA from whole brain of Cane Toad, B19
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756315
...
+
B208386cane toadmarine toadRhinella marina Description:RNA from whole brain of Cane Toad, B20
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756316
...
+
B318386cane toadmarine toadRhinella marina Description:RNA from whole brain of Cane Toad, B31
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756317
...
+
B328386cane toadmarine toadRhinella marina Description:RNA from whole brain of Cane Toad, B32
Alternative names:cane toad
Alternative accession-BioSample:SAMN6756318
...
+
RM0021M8386cane toadmarine toadRhinella marina Description:Total RNA from triceps femoris muscle ...
Alternative names:cane toad
Alternative accession-BioSample:SAMN3401027
...
+
RM0094M8386cane toadmarine toadRhinella marina Description:Total RNA from triceps femoris muscle ...
Alternative names:cane toad
Alternative accession-BioSample:SAMN3401035
...
+
RM0108M8386cane toadmarine toadRhinella marina Description:Total RNA from triceps femoris muscle ...
Alternative names:cane toad
Alternative accession-BioSample:SAMN3401037
...
+
RM0169M8386cane toadmarine toadRhinella marina Description:Total RNA from triceps femoris muscle ...
Alternative names:cane toad
Alternative accession-BioSample:SAMN3401041
...
+
Displaying 1-10 of 19 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
annotationGFF64.84 MB2017-11-01
Coding SequenceFASTA21.36 MB2017-11-01
Displaying 11-12 of 12 File(s).

History:

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