Sequencing, Annotation and Analysis of the Syrian Hamster (<i>Mesocricetus auratus</i>) Transcriptome

<div><p>Background</p><p>The Syrian hamster (golden hamster, <i>Mesocricetus auratus</i>) 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.</p><p>Results</p><p>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 <i>Mesocricetus auratus</i> 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.</p><p>Conclusions</p><p>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.</p></div

Distogram showing the commonly mapped transcripts and phylogenetic tree showing the divergences amongst the different species.

<p>(A) Distogram showing the number of transcripts commonly mapped by the Syrian hamster transcriptome between the different species used in this study. Each cell of the distogram represents the number of transcripts commonly mapped by two different species using a gradient color. (B) Phylogenetic tree showing the genomic divergence between a subset of the different species used in this study. Each leaf of the tree represents a different species and the distances of the edges are proportional to the genomic distances between the species. Genomic distances have been calculated based on the list of 611 Syrian hamster contigs and singletons that have been commonly aligned on the transcriptome references of the 13 species having the highest number of commonly aligned sequences.</p

Functional enrichment of the mouse genes mapped by our transcriptome assembly.

<p>List of the top 5 biological functions and the top 5 canonical pathways found as statistically over-represented based on the list of 9,546 mouse genes mapped by our transcriptome assembly. The range of p-values is indicated for the biological functions and the p-value is indicated for each canonical pathways.</p><p>Functional enrichment of the mouse genes mapped by our transcriptome assembly.</p

List of the top 50 expressed genes in the library.

<p>For each of the top 50 expressed genes in the library, based on the mouse annotations, the Ensembl mouse gene identified, the associated gene name, description, and the number of count (number of time that the genes have been mapped by the reads) are indicated.</p><p>List of the top 50 expressed genes in the library.</p

Transcriptome references and alignment statistics.

<p>For each transcriptome reference used in this study, the name of the species, the number of genes available, and the number of transcripts available are indicated.</p><p>*The number of available transcripts indicated for the Chinese hamster ovary cells represents the number of available transcript fragments available and not the number of distinct transcripts. Moreover, for each transcriptome reference used in this study, the number of aligned contigs and singletons, the number of mapped transcripts and the number of mapped genes are indicated. The percentages of mapped transcripts and mapped genes relative to the total number of transcripts and genes available on the transcriptome references are provided. Moreover the percentage of alignments relative to the total number of contigs and singletons in our library (174,278) is also provided.</p><p>Transcriptome references and alignment statistics.</p

Erythropoietin levels increase during cerebral malaria and with severity of the infection.

<p>(A) Erythropoietin (EPO) levels were measured in the plasma of endemic controls (EC), mild malaria (MM) and severe malaria (SM) patients, and (B) in the SM sub-groups of non-cerebral malaria (NCM) and cerebral malaria (CM). (C) EPO levels were compared between CM patients who survived and those who did not. Significant differences with the EC group or between selected groups are indicated as the following: *<i>p</i> ≤ 0.05; **<i>p</i> ≤ 0.01; ***<i>p</i> ≤ 0.001.</p

Pie diagrams showing the alignment positions of the contigs and singletons on the mouse and rat transcript regions.

<p>(A) Pie diagram showing the distribution of alignment positions of the 41,651 contigs and singletons on the mouse transcripts regions (5′ UTR, coding region, 3′ UTR, or inter-region). (B) Pie diagram showing the distribution of alignment positions of the 26,258 contigs and singletons on the rat transcripts regions. For each species and transcript region the number and percentage of aligned sequences are indicated.</p

Baseline characteristics.

<p>Baseline characteristics.</p

Correlation of EPO plasma levels, with cytokines.

<p>Correlation of EPO plasma levels, with cytokines.</p

Schematic representation of the top two over-represented canonical pathways in our transcriptome assembly.

<p>(A) Representation of the “Protein Ubiquitination” canonical pathway. (B) Representation of the “Molecular Mechanisms of Cancer” canonical pathway. Both pathways have been generated based on mouse annotations. Transcripts involved in these pathways are indicated by different node shapes and associations are indicated by different edge shapes. Legends for the different nodes and edges are given in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112617#pone.0112617.s001" target="_blank">Figure S1</a></b>. For both pathways, transcripts present in our library are indicated in gray. Associated p-values showing the statistical over-representation significance of the canonical pathways are also indicated.</p