Marmota monax
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA85015 | ENA |
REPOSITORIES: ENA
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Project description:cross-hybridization of woodchuck HCCs using human, rat and mouse arrays
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Project description:The Eastern woodchuck (Marmota monax) is a classical animal model for studying hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) in humans. Recently, we found that Marmota himalayana, an Asian animal species closely related to Marmota monax, is susceptible to woodchuck hepatitis virus (WHV) infection and can be used as a new mammalian model for HBV infection. However, the lack of genomic sequence information of both Marmota models strongly limited their application breadth and depth. To address this major obstacle of the Marmota models, we utilized Illumina RNA-Seq technology to sequence the cDNA libraries of liver and spleen samples of two Marmota monax and four Marmota himalayana. In total, over 13 billion nucleotide bases were sequenced and approximately 1.5 billion clean reads were obtained. Following assembly, 106,496 consensus sequences of Marmota monax and 78,483 consensus sequences of Marmota himalayana were detected. For functional annotation, in total 73,603 Unigenes of Marmota monax and 78,483 Unigenes of Marmota himalayana were identified using different databases (NR, NT, Swiss-Prot, KEGG, COG, GO). The Unigenes were aligned by blastx to protein databases to decide the coding DNA sequences (CDS) and in total 41,247 CDS of Marmota monax and 34,033 CDS of Marmota himalayana were predicted. The single nucleotide polymorphisms (SNPs) and the simple sequence repeats (SSRs) were also analyzed for all Unigenes obtained. Moreover, a large-scale transcriptome comparison was performed and revealed a high similarity in transcriptome sequences between the two marmota species. Our study provides an extensive amount of novel sequence information for Marmota monax and Marmota himalayana. This information may serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the identification and characterization of functional genes that are involved in WHV infection and HCC development in the woodchuck model.
| S-EPMC5091844 | biostudies-literature
Project description:We sequenced the genome of the North American groundhog, Marmota monax, also known as the woodchuck. Our sequencing strategy included a combination of short, high-quality Illumina reads plus long reads generated by both Pacific Biosciences and Oxford Nanopore instruments. Assembly of the combined data produced a genome of 2.74 Gbp in total length, with an N50 contig size of 1,094,236 bp. To annotate the genome, we mapped the genes from another M. monax genome and from the closely related Alpine marmot, Marmota marmota, onto our assembly, resulting in 20,559 annotated protein-coding genes and 28,135 transcripts. The genome assembly and annotation are available in GenBank under BioProject PRJNA587092.
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Project description:Mammalian hibernation is a unique strategy for winter survival in response to limited food supply and harsh climate, which includes resistance to cardiac arrhythmias. We previously found that hibernating woodchucks (Marmota monax) exhibit natural resistance to Ca2+ overload-related cardiac dysfunction and nitric oxide (NO)-dependent vasodilation, which maintains myocardial blood flow during hibernation. Since the cellular/molecular mechanisms mediating the protection are less clear, the goal of this study was to investigate changes in the heart proteome and reveal related signaling networks that are involved in establishing cardioprotection in woodchucks during hibernation. This was accomplished using isobaric tags for a relative and absolute quantification (iTRAQ) approach. The most significant changes observed in winter hibernation compared to summer non-hibernation animals were upregulation of the antioxidant catalase and inhibition of endoplasmic reticulum (ER) stress response by downregulation of GRP78, mechanisms which could be responsible for the adaptation and protection in hibernating animals. Furthermore, protein networks pertaining to NO signaling, acute phase response, CREB and NFAT transcriptional regulations, protein kinase A and α-adrenergic signaling were also dramatically upregulated during hibernation. These adaptive mechanisms in hibernators may provide new directions to protect myocardium of non-hibernating animals, especially humans, from cardiac dysfunction induced by hypothermic stress and myocardial ischemia.
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Project description:Intrahepatic transcriptional signature associated with response to interferon-a treatment in the woodchuck model of chronic hepatitis B
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Project description:Identification of an intrahepatic transcriptional signature associated with self-limiting infection in the woodchuck model of hepatitis B
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Project description:Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Spleen gene expression in uninfected, resolved and chronically infected woodchucks
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