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

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 ann...

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Autores principales: Hobbs, Matthew, Pavasovic, Ana, King, Andrew G, Prentis, Peter J, Eldridge, Mark DB, Chen, Zhiliang, Colgan, Donald J, Polkinghorne, Adam, Wilkins, Marc R, Flanagan, Cheyne, Gillett, Amber, Hanger, Jon, Johnson, Rebecca N, Timms, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247155/
https://www.ncbi.nlm.nih.gov/pubmed/25214207
http://dx.doi.org/10.1186/1471-2164-15-786
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author Hobbs, Matthew
Pavasovic, Ana
King, Andrew G
Prentis, Peter J
Eldridge, Mark DB
Chen, Zhiliang
Colgan, Donald J
Polkinghorne, Adam
Wilkins, Marc R
Flanagan, Cheyne
Gillett, Amber
Hanger, Jon
Johnson, Rebecca N
Timms, Peter
author_facet Hobbs, Matthew
Pavasovic, Ana
King, Andrew G
Prentis, Peter J
Eldridge, Mark DB
Chen, Zhiliang
Colgan, Donald J
Polkinghorne, Adam
Wilkins, Marc R
Flanagan, Cheyne
Gillett, Amber
Hanger, Jon
Johnson, Rebecca N
Timms, Peter
author_sort Hobbs, Matthew
collection PubMed
description 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 non-redundant 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-B-like 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-786) contains supplementary material, which is available to authorized users.
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spelling pubmed-42471552014-11-29 A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity Hobbs, Matthew Pavasovic, Ana King, Andrew G Prentis, Peter J Eldridge, Mark DB Chen, Zhiliang Colgan, Donald J Polkinghorne, Adam Wilkins, Marc R Flanagan, Cheyne Gillett, Amber Hanger, Jon Johnson, Rebecca N Timms, Peter BMC Genomics Research Article 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 non-redundant 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-B-like 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-786) contains supplementary material, which is available to authorized users. BioMed Central 2014-09-11 /pmc/articles/PMC4247155/ /pubmed/25214207 http://dx.doi.org/10.1186/1471-2164-15-786 Text en © Hobbs et al.; licensee BioMed Central Ltd. 2014 This article is published under license to 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.
spellingShingle Research Article
Hobbs, Matthew
Pavasovic, Ana
King, Andrew G
Prentis, Peter J
Eldridge, Mark DB
Chen, Zhiliang
Colgan, Donald J
Polkinghorne, Adam
Wilkins, Marc R
Flanagan, Cheyne
Gillett, Amber
Hanger, Jon
Johnson, Rebecca N
Timms, Peter
A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
title A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
title_full A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
title_fullStr A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
title_full_unstemmed A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
title_short A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
title_sort transcriptome resource for the koala (phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247155/
https://www.ncbi.nlm.nih.gov/pubmed/25214207
http://dx.doi.org/10.1186/1471-2164-15-786
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