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

Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF, Feldmann H, Ebihara H, Katze MG - PLoS ONE (2014)

Bottom Line: Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons).Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library.Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, United States of America.

ABSTRACT

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.

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.

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Related in: MedlinePlus

Histograms showing the length distribution of the reads and the length distribution of the singletons and contigs.(A) The length distribution of the reads is shown in a gray histogram. Bins of the histogram have been set to 50 nucleotides. The lengths of the reads range from 40 to 631, with a median length of 387 and a mean length of 352. The reads represents a total of 426,683,712 nucleotides bases. (B) The length distribution of the 111,796 singletons is shown in a red histogram while the length distribution of the 62,482 contigs is shown in a blue histogram. Bins of the histograms have been set to 25 nucleotides. The lengths of the singleton sequences range from 50 to 614, with a median length of 187 and a mean length of 265. The lengths of the contig sequences range from 50 to 4,054, with a median length of 473 and a mean length of 487. Our Syrian hamster transcriptome represents a total of 60,117,204 nucleotides bases.
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pone-0112617-g001: Histograms showing the length distribution of the reads and the length distribution of the singletons and contigs.(A) The length distribution of the reads is shown in a gray histogram. Bins of the histogram have been set to 50 nucleotides. The lengths of the reads range from 40 to 631, with a median length of 387 and a mean length of 352. The reads represents a total of 426,683,712 nucleotides bases. (B) The length distribution of the 111,796 singletons is shown in a red histogram while the length distribution of the 62,482 contigs is shown in a blue histogram. Bins of the histograms have been set to 25 nucleotides. The lengths of the singleton sequences range from 50 to 614, with a median length of 187 and a mean length of 265. The lengths of the contig sequences range from 50 to 4,054, with a median length of 473 and a mean length of 487. Our Syrian hamster transcriptome represents a total of 60,117,204 nucleotides bases.

Mentions: The brains, lungs, spleens, kidneys, livers, and hearts were collected from three adult female Syrian hamsters. Total RNAs were isolated, pooled, and contaminating genomic DNA removed. Following adaptor ligation, cDNAs were 3′ fragment-sequenced on a Roche 454 GS FLX Titanium instrument. The sequencing generated 1,283,840 reads with an average length of 344 bases. Reads were trimmed for quality and reads shorter than 40 bases were discarded, resulting in 1,212,395 sequence reads available for further assembly and analysis. Figure 1A shows the length distribution of reads before assembly. Consistent with most of the publicly available transcriptome libraries [29], we observed that our reads ranged between 200 and 600 nucleotides in length.


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

Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF, Feldmann H, Ebihara H, Katze MG - PLoS ONE (2014)

Histograms showing the length distribution of the reads and the length distribution of the singletons and contigs.(A) The length distribution of the reads is shown in a gray histogram. Bins of the histogram have been set to 50 nucleotides. The lengths of the reads range from 40 to 631, with a median length of 387 and a mean length of 352. The reads represents a total of 426,683,712 nucleotides bases. (B) The length distribution of the 111,796 singletons is shown in a red histogram while the length distribution of the 62,482 contigs is shown in a blue histogram. Bins of the histograms have been set to 25 nucleotides. The lengths of the singleton sequences range from 50 to 614, with a median length of 187 and a mean length of 265. The lengths of the contig sequences range from 50 to 4,054, with a median length of 473 and a mean length of 487. Our Syrian hamster transcriptome represents a total of 60,117,204 nucleotides bases.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4232415&req=5

pone-0112617-g001: Histograms showing the length distribution of the reads and the length distribution of the singletons and contigs.(A) The length distribution of the reads is shown in a gray histogram. Bins of the histogram have been set to 50 nucleotides. The lengths of the reads range from 40 to 631, with a median length of 387 and a mean length of 352. The reads represents a total of 426,683,712 nucleotides bases. (B) The length distribution of the 111,796 singletons is shown in a red histogram while the length distribution of the 62,482 contigs is shown in a blue histogram. Bins of the histograms have been set to 25 nucleotides. The lengths of the singleton sequences range from 50 to 614, with a median length of 187 and a mean length of 265. The lengths of the contig sequences range from 50 to 4,054, with a median length of 473 and a mean length of 487. Our Syrian hamster transcriptome represents a total of 60,117,204 nucleotides bases.
Mentions: The brains, lungs, spleens, kidneys, livers, and hearts were collected from three adult female Syrian hamsters. Total RNAs were isolated, pooled, and contaminating genomic DNA removed. Following adaptor ligation, cDNAs were 3′ fragment-sequenced on a Roche 454 GS FLX Titanium instrument. The sequencing generated 1,283,840 reads with an average length of 344 bases. Reads were trimmed for quality and reads shorter than 40 bases were discarded, resulting in 1,212,395 sequence reads available for further assembly and analysis. Figure 1A shows the length distribution of reads before assembly. Consistent with most of the publicly available transcriptome libraries [29], we observed that our reads ranged between 200 and 600 nucleotides in length.

Bottom Line: Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons).Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library.Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, United States of America.

ABSTRACT

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.

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.

Show MeSH
Related in: MedlinePlus