richardson-improvingamphibian-2018.pdf (350.57 kB)
Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader
journal contribution
posted on 2018-01-01, 00:00 authored by Mark RichardsonMark Richardson, F Sequeira, Daniel Selechnik, M Carneiro, M Vallinoto, J G Reid, Andrea West, M R Crossland, R Shine, Lee RollinsBackground: 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.
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Journal
GigaScienceVolume
7Issue
1Pagination
1 - 7Publisher
Oxford University PressLocation
Oxford, Eng.Publisher DOI
ISSN
2047-217XeISSN
2047-217XLanguage
engPublication classification
C1 Refereed article in a scholarly journal; C Journal articleCopyright notice
2017, The AuthorUsage metrics
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