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

作者：Matthew Hobbs, Ana Pavasovic, Andrew King, Peter J. Prentis, Mark D. B. Eldridge, Zhiliang Chen, D. J. Colgan, Adam Polkinghorne, Marc R. Wilkins, Cheyne Flanagan, Amber Gillett, Jon Hanger, Rebecca N. Johnson, Peter Timms · 发表于：BMC Genomics · 年份：2014 · DOI：10.1186/1471-2164-15-786 · 被引用次数：56 · 研究领域：Chromosomal and Genetic Variations、Evolution and Paleontology Studies、Genetic Mapping and Diversity in Plants and Animals

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 transcript...