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Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome

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      Abstract

      BackgroundThe Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species.ResultsA cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species.ConclusionsThis Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.

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            Author and article information

            Affiliations
            [1 ]Department of Microbiology, University of Washington, Seattle, Washington, United States of America
            [2 ]Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
            [3 ]Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
            [4 ]Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
            Ecole Normale Supérieure de Lyon, France
            Author notes

            Competing Interests: The authors have declared that no competing interests exist.

            Conceived and designed the experiments: DS ALR HF HE MGK. Performed the experiments: KV DS. Analyzed the data: NT CM. Contributed reagents/materials/analysis tools: DS KV SFP. Wrote the paper: NT DS ALR CM SFP HE.

            Contributors
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, USA )
            1932-6203
            2014
            14 November 2014
            : 9
            : 11
            25398096
            4232415
            PONE-D-14-27735
            10.1371/journal.pone.0112617
            (Editor)

            This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

            Counts
            Pages: 11
            Funding
            This work was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health and the NIAID Regional Centers of Excellence (U54 AI081680) to MGK. The funders were not involved in the study design, data collection and analysis, or preparation of the manuscript. NIAID was solely involved in the decision to publish.
            Categories
            Research Article
            Biology and Life Sciences
            Computational Biology
            Genome Analysis
            Sequence Assembly Tools
            Transcriptome Analysis
            Comparative Genomics
            Population Modeling
            Evolutionary Biology
            Evolutionary Systematics
            Phylogenetics
            Animal Phylogenetics
            Genetics
            Genomics
            Animal Genomics
            Microbiology
            Animal Models of Infection
            Medicine and Health Sciences
            Infectious Diseases
            Research and Analysis Methods
            Animal Studies
            Animal Models of Disease
            Custom metadata
            The authors confirm that all data underlying the findings are fully available without restriction. The unassembled reads have been uploaded on the NCBI-SRA database [45] and are available via the BioProject SRP032520. Moreover, we released the annotated transcriptome assembly in LabArchives ( http://www.labarchives.com/) and are available via the DOI http://dx.doi.org/10.6070/H4FQ9TKP.

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