Draft genome assembly of the invasive cane toad, Rhinella marina

Abstract

BackgroundThe 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.FindingsWe report a draft genome assembly for R. marina, the first of its kind for the Bufonidae family. We used a combination of long-read Pacific Biosciences RS II and short-read Illumina HiSeq X sequencing to generate 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 Swiss-Prot. Repeat sequences were estimated to account for 63.9% of the assembly.ConclusionsThe 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.

Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association

“…This result is particularly noteworthy as the previously identified amphibian influenza virus, Wuhan asiatic toad influenza virus, was more closely related to IBV [3]. Cane toad influenza-like virus was identified in four larval samples of cane toad (Rhinella marina), from two geographic locations in Australia: Innisfail, Queensland, Australia (SRA accessions: SRR5446725, SRR5446726) and Oombulgurri, Western Australia, Australia (SRA accessions: SRR5446727, SRR5446728) [50]. We did not identify any virus reads in any adult tissue samples taken in Australia nor from libraries constructed from cane toad samples from Macapa city, Brazil, from the same study [50].…”

Determinants and Consequences of Dispersal in Vertebrates with Complex Life Cycles: A Review of Pond-Breeding Amphibians

“…They can be reared easily in the laboratory and used to address questions about dispersal experimentally. In addition, many populations can be surveyed using demographic and genetic tools (Cayuela et al 2018b), and the genomes of some species are well described (Hellsten et al 2010;Edwards et al 2018;Nowoshilow et al 2018). Additionally, a comprehensive understanding of dispersal in this group is key in supporting evidence-based conservation, a pressing global issue since amphibians are the most threatened class of vertebrates (Catenazzi 2015).…”

Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses

“…In GenomeScope v1, the default for CovMax is set to 1k. This low default threshold may explain why, in studies with vanilla [40], cane toad [41], and pacific oyster [18,42], k-mer based GenomeScope estimates of genome sizes were only half of those obtained by flow cytometry analyses and considerably smaller than those obtained after genome assembly. For rooibos, GenomeScope estimates differed between 0.51 and 1.01 Gbp, indicating that with this program parameter settings must be adjusted, based on reasonable assumptions on the genome under investigation (repeat content, data preprocessing).…”