Supporting data for "Draft genome assembly of the invasive cane toad, Rhinella marina"

Dataset type: Genomic
Data released on July 23, 2018

Edwards RJ; Enosi Tuipulotu D; Amos TG; O’Meally D; Richardson MF; Russell TL; Vallinoto M; Carneiro M; Ferrand N; Wilkins MR; Sequeira F; Rollins LA; Holmes EC; Shine R; White PA (2018): Supporting data for "Draft genome assembly of the invasive cane toad, Rhinella marina" GigaScience Database. http://dx.doi.org/10.5524/100483

DOI10.5524/100483

The cane toad (Rhinella marina formerly Bufo marinus) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research.
We report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long read PacBio RS II and short read Illumina HiSeq X sequencing to generate a total of 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n=3950), illustrating that the gene-containing regions have been well-assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in SwissProt. Repeat sequences were estimated to account for 63.9% of the assembly.
The R. marina draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.

Additional details

Read the peer-reviewed publication(s):

Edwards, R. J., Tuipulotu, D. E., Amos, T. G., O’Meally, D., Richardson, M. F., Russell, T. L., … White, P. A. (2018). Draft genome assembly of the invasive cane toad, Rhinella marina. GigaScience, 7(9). doi:10.1093/gigascience/giy095

Related datasets:

doi:10.5524/100483 HasPart doi:10.5524/100374

Additional information:

http://www.slimsuite.unsw.edu.au/servers/apollo.php

Accessions (data generated as part of this study):

BioProject: PRJEB24695





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMEA1045582868386cane toadmarine toadRhinella marina Description:High molecular weight DNA extraction f...
Tissue:liver
Life stage:adult
...
+
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
TextUNKNOWN7.71 KB2018-07-16
mixed archiveUNKNOWN124.52 MB2018-07-16
Genome sequenceFASTA662.54 MB2018-07-16
AlignmentsFASTA40.62 MB2018-07-16
protein sequenceFASTA2.57 MB2018-07-16
protein sequenceFASTA4.97 MB2018-07-16
Phylogenetic treeUNKNOWN64.69 MB2018-07-16
annotationGFF12.65 MB2018-07-16
MD5sumUNKNOWN0.69 KB2018-07-16
protein sequenceFASTA12.88 MB2018-07-16
Displaying 1-10 of 13 File(s).
Funding body Awardee Award ID Comments
Australian Research Council L A Rollins DE150101393 DECRA Fellowship
Australian Research Council R Shine FL120100074 Australian Laureate Fellowship
Australian Research Council E C Holmes FL170100022 Australian Laureate Fellowship
Australian Research Council M R Wilkins LE150100031
Fundação para a Ciência e a Tecnologia M Carneiro IF/00283/2014/CP1256/CT0012 FCT investigator grant
Brazilian National Council for Scientific and Technological Development M Vallinoto 302892/2016-8 CNPq fellowship
Bioplatforms Australia E C Holmes
Australian Research Council R Shine DP160102991
Fundação para a Ciência e a Tecnologia F Sequeira UID/BIA/50027/2013
Fundo Europeu De Desenvolvimento Regional F Sequeira COMPETE, POCI-01-0145-FEDER-006821
Date Action
July 23, 2018 Dataset publish
July 23, 2018 Title updated from : Supporting data for "Draft genome assembly of the invasive cane toad, Rhinella marina"
July 23, 2018 Title updated from : Supporting data for "Draft genome assembly of the invasive cane toad, Rhinella marina"
September 19, 2018 File readme.txt updated
August 22, 2018 Manuscript Link added : 10.1093/gigascience/giy095