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

• Published in: PloS one Vol. 9; no. 11; p. e112617
• Main Authors: Tchitchek, Nicolas, Safronetz, David, Rasmussen, Angela L, Martens, Craig, Virtaneva, Kimmo, Porcella, Stephen F, Feldmann, Heinz, Ebihara, Hideki, Katze, Michael G
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 14.11.2014; Public Library of Science (PLoS)
• Subjects: Analysis; Animals; Annotations; Base Sequence; Biological activity; Biology and Life Sciences; Cricetinae; Ebola virus; Ebolavirus; Evolution; Female; Gene expression; Gene Library; Gene sequencing; Genes; Genomes; Genomics; Hamsters; Immunology; Infectious diseases; Kidneys; Laboratories; Life Sciences; Lungs; Medicine and Health Sciences; Mesocricetus - genetics; Mesocricetus auratus; Mice; Molecular Sequence Annotation; Molecular Sequence Data; Nucleotides; Phylogenetics; Rats; Research and Analysis Methods; RNA; Rodents; Sequence Analysis, DNA; snRNA; Species; Species Specificity; Transcriptome - genetics; Viral diseases; Virology; Viruses; Zoonoses; Cricetinae; Mesocricetus/genetics; Gene Library; Species Specificity; Molecular Sequence Annotation; Molecular Sequence Data; Rats; Transcriptome/genetics; Animals; Base Sequence; DNA; Female; Mice; Sequence Analysis
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0112617

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. 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. 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.