Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader

Mark F. Richardson*, Fernando Sequeira, Daniel Selechnik, Miguel Carneiro, Marcelo Vallinoto, Jack G. Reid, Andrea J. West, Michael R. Crossland, Richard Shine, Lee A. Rollins

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
6 Downloads (Pure)

Abstract

Background: Cane toads (Rhinella marina) are an iconic invasive species introduced to 4 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. Findings: Using approximately 1.9 billion reads from developing tadpoles and 6 adult tissue-specific cDNA libraries, as well as 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 Benchmarking Universal Single-Copy Orthologs data set. Robust assembly metrics and comparisons with several available anuran transcriptomes and genomes indicate that our cane toad assembly is one of the most complete anuran genomic resources available. Conclusions: 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 data set is publically available in NCBI and GigaDB to serve as a resource for other researchers.

Original languageEnglish
Pages (from-to)1-7
Number of pages7
JournalGigaScience
Volume7
Issue number1
DOIs
Publication statusPublished - 1 Jan 2018
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2017. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • de novo assembly
  • Bufo marinus
  • cane toad
  • Rhinella marina
  • invasive species
  • RNA-Seq
  • transcriptome
  • anuran
  • amphibian
  • Anuran
  • Transcriptome
  • Cane toad
  • Invasive species
  • Amphibian

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