IGTCM

IGTCM integrates genomic and chemical data for Traditional Chinese Medicines to provide an annotated resource linking 83 TCM-related plant genomes, ~3.6 million genes, ~3.5 million proteins (with CDS), >4 million RNA sequences and 1,033 non-redundant chemical component records to pathway and functional annotations.

Key Features:

• Genomic corpus: Contains 83 annotated genomes and over 14 million records covering TCM-related plants.
• Sequence inventory: Includes approximately 3.6 million genes, 3.5 million proteins with coding sequences (CDS), and more than 4 million RNA sequences.
• Chemical component integration: Integrates 1,033 non-redundant component records for 68 herbs obtained from established databases such as GenBank and RefSeq.
• Functional annotation: Annotates genes, proteins, and components using eggNOG-mapper and KEGG to provide pathway information and enzyme classifications.
• Sequence similarity search: Supports sequence similarity searches for comparative analyses and gene/component identification.
• Visualization: Provides visualization capabilities for exploring genomic, transcriptomic, and component relationships.
• Cross-species linkage: Enables cross-species and component linkage analysis to connect genes and compounds across TCM plants.

Scientific Applications:

• Biosynthesis pathway analysis: Facilitates exploration of biosynthetic pathways for medicinal compounds using KEGG and functional annotations.
• Gene identification for bioactive compounds: Supports identification of genes involved in production of bioactive compounds through integrated genome and component data.
• Molecular breeding: Enables selection of candidate genes for molecular breeding to improve TCM-related plant traits.
• Drug discovery: Serves as a resource to link plant genes and chemical components for drug discovery research.
• Conservation and utilization: Informs protection and rational utilization of TCM plant genetic and chemical resources.

Methodology:

Records were downloaded and integrated from GenBank and RefSeq; genes, proteins and components were annotated with eggNOG-mapper and KEGG to obtain pathway and enzyme classifications; sequence similarity search and visualization functions support data exploration.