Abstract
BackgroundMarmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integrative database is urgent needed.DescriptioniMarmot is freely available on the web at http://www.marmotdb.org/ and currently contains the biological information of 14 marmots, genomic sequence of 6 marmots, syntenic relationship and orthologs among 3 marmots, and expression profiles of several hibernators and plague hosts. To assist with the genomic and transcriptomic analysis, we also integrated a set of analysis and visualization tools, such as KEGG or GO enrichment analysis, PCA, Blast, Muscle, GeneWise, Lastz, and JBrowse. Particularly, one DEGs (differentially expressed genes) module has been implemented in this database to visualize the gene expression changes in hibernators and plague hosts.ConclusionThis database will provide comprehensive information and analysis platform for researchers interested in understanding the biological features of marmots.
Highlights
Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields
To facilitate the usage and application of these genomic, transcriptomic data and comparative results, we have developed the marmot database as a highly integrative information platform with online analysis tools
The assembly sequence of Alpine marmot and Yellow-bellied marmot were downloaded from the GenBank assembly database of National Center for Biotechnology Information (NCBI), while the assembly of Himalayan marmot was derived from our previous work [10]
Summary
Marmots have been known since antiquity and firstly recognized by Thorington and Hoffman [1]. To facilitate the usage and application of these genomic, transcriptomic data and comparative results, we have developed the marmot database (iMarmot: www.marmotdb.org) as a highly integrative information platform with online analysis tools. The assembly sequence of Alpine marmot and Yellow-bellied marmot were downloaded from the GenBank assembly database of NCBI, while the assembly of Himalayan marmot was derived from our previous work [10]. 19,470 protein-coding genes were annotated for Himalayan marmot, 20,832 for Alpine marmot genome and 20,217 for Yellow-bellied marmot genome. Genomic variations The iMarmot database currently contains high quality SNP data of 5 marmots, including an albinistic Himalayan marmot, Long-tailed marmot, Gray marmot, Yellow-bellied marmot, and Mongolian marmot.
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