Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome

Nicolas Tchitchek, David Safronetz, Angela L. Rasmussen, Craig Martens, Kimmo Virtaneva, Stephen F. Porcella, Heinz Feldmann, Hideki Ebihara, Michael G. Katze

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Results: A 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.

Conclusions: This 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.

Background: The 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.

Original languageEnglish (US)
Article numbere112617
JournalPLoS One
Volume9
Issue number11
DOIs
StatePublished - Nov 14 2014
Externally publishedYes

Fingerprint

Mesocricetus
Transcriptome
transcriptome
Genes
Small Nuclear RNA
Pathogens
Microarrays
Gene Library
Liver
Genome
Rats
Brain
Animals
Nucleotides
Libraries
genome
Cells
Mesocricetus auratus
Messenger RNA
small nuclear RNA

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Tchitchek, N., Safronetz, D., Rasmussen, A. L., Martens, C., Virtaneva, K., Porcella, S. F., ... Katze, M. G. (2014). Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PLoS One, 9(11), [e112617]. https://doi.org/10.1371/journal.pone.0112617

Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. / Tchitchek, Nicolas; Safronetz, David; Rasmussen, Angela L.; Martens, Craig; Virtaneva, Kimmo; Porcella, Stephen F.; Feldmann, Heinz; Ebihara, Hideki; Katze, Michael G.

In: PLoS One, Vol. 9, No. 11, e112617, 14.11.2014.

Research output: Contribution to journalArticle

Tchitchek, N, Safronetz, D, Rasmussen, AL, Martens, C, Virtaneva, K, Porcella, SF, Feldmann, H, Ebihara, H & Katze, MG 2014, 'Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome', PLoS One, vol. 9, no. 11, e112617. https://doi.org/10.1371/journal.pone.0112617
Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF et al. Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PLoS One. 2014 Nov 14;9(11). e112617. https://doi.org/10.1371/journal.pone.0112617
Tchitchek, Nicolas ; Safronetz, David ; Rasmussen, Angela L. ; Martens, Craig ; Virtaneva, Kimmo ; Porcella, Stephen F. ; Feldmann, Heinz ; Ebihara, Hideki ; Katze, Michael G. / Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. In: PLoS One. 2014 ; Vol. 9, No. 11.
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