iMarmot

iMarmot provides an integrative database for comparative and functional genomics of marmots, consolidating genomic sequences, synteny, orthologs, expression profiles, and differential expression analyses to support evolutionary and disease-related research.

Key Features:

• Species coverage: Contains extensive biological information on 14 marmot species.
• Genomic data: Includes genomic sequences for six marmot species to facilitate comparative analyses.
• Syntenic relationships and orthologs: Provides synteny maps and orthologous gene relationships among three marmot species.
• Expression profiles: Hosts expression datasets from various hibernators and plague hosts for comparative transcriptomics.
• Differentially Expressed Genes (DEGs) module: Enables visualization and analysis of gene expression changes in hibernators and plague hosts.
• Sequence alignment tools: Supports sequence comparison using BLAST, Muscle, GeneWise, and Lastz.
• Genome browser: Integrates JBrowse for genome-level visualization of annotations and sequence features.

Scientific Applications:

• Comparative genomics: Enables analysis of genomic sequences, synteny, and orthologs to study evolutionary relationships among marmots.
• Functional genomics: Uses expression profiles and DEGs analyses to investigate gene function and regulatory changes during hibernation and in response to plague.
• Public health and zoonosis research: Supports studies on marmot-associated plague and zoonotic disease transmission through integrated genomic and expression data.

Methodology:

The platform performs KEGG and GO enrichment analysis, Principal Component Analysis (PCA), sequence alignment using BLAST, Muscle, GeneWise, and Lastz, and genome visualization with JBrowse.