A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity

Matthew Hobbs; Ana Pavasovic; Andrew G King; Peter J Prentis; Mark D B Eldridge; Zhiliang Chen; Donald J Colgan; Adam Polkinghorne; Marc R Wilkins; Cheyne Flanagan; Amber Gillett; Jon Hanger; Rebecca N Johnson; Peter Timms

doi:10.1186/1471-2164-15-786

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A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity

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A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity

Matthew Hobbs, Ana Pavasovic, Andrew G King, Peter J Prentis, Mark D B Eldridge, Zhiliang Chen, Donald J Colgan, Adam Polkinghorne, Marc R Wilkins, Cheyne Flanagan, …

BMC Genomics, Vol.15, 786

2014

DOI: https://doi.org/10.1186/1471-2164-15-786

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Abstract

transcriptome

koala

phascolarctos cinereus

koala retrovirus

alpha amylase

aldehyde reductase

Background: The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results: RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a nonredundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-Blike sequence in a wild population. Conclusions: This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org.

Details

Title: A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
Authors: Matthew Hobbs (Author) - Australian Museum
Ana Pavasovic (Author) - Queensland University of Technology
Andrew G King (Author) - Australian Museum
Peter J Prentis (Author) - Queensland University of Technology
Mark D B Eldridge (Author) - Australian Museum
Zhiliang Chen (Author) - University of New South Wales
Donald J Colgan (Author) - Australian Museum
Adam Polkinghorne (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Marc R Wilkins (Author) - University of New South Wales
Cheyne Flanagan (Author) - Port Macquarie Koala Hospital
Amber Gillett (Author) - Australia Zoo Wildlife Hospital
Jon Hanger (Author) - Endeavour Veterinary Ecology Pty Ltd
Rebecca N Johnson (Author) - Australian Museum
Peter Timms (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Publication details: BMC Genomics, Vol.15, 786; 16
Publisher: BioMed Central Ltd.
Date published: 2014
DOI: 10.1186/1471-2164-15-786
ISSN: 1471-2164
Copyright note: Copyright © 2014 Hobbs et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99448931002621
Output Type: Journal article

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