TCOD

TCOD integrates multi-omics datasets for 15 tropical crop species to support genomic selective breeding and trait biology by providing chromosome-level assemblies, annotated genes, variant and transcriptomic data, and germplasm records.

Key Features:

• Comprehensive Data Integration: Consolidates diverse omics datasets from 15 tropical crop species, including 34 chromosome-level de novo assemblies.
• Extensive Genomic Resources: Hosts 1,255,004 genes with functional annotations.
• Variant Data: Contains 282,436,992 unique variants derived from 2,048 whole-genome sequencing samples.
• Transcriptomic Information: Includes 88 transcriptomic profiles generated from 1,997 RNA-Seq samples.
• Germplasm Collection: Features data on 13,381 germplasm items to support breeding programs.

Scientific Applications:

• Genomic selective breeding: Supports identification and comparison of candidate genes and variants for breeding programs in tropical crops.
• Trait biology and improvement: Enables investigations of traits to improve crop resilience, productivity, and adaptability.
• Comparative genomics: Enables cross-species comparisons based on homologous relationships using gene-centric integration.
• Genetic diversity and variation analysis: Facilitates analysis of genetic diversity using WGS-derived variant datasets.
• Transcriptome analysis: Supports exploration of gene expression patterns across conditions and species using RNA-Seq profiles.
• Germplasm-based breeding: Integrates germplasm records to inform breeding strategies.

Methodology:

TCOD uses genes as central nodes to interconnect omics datasets and enable cross-species comparisons based on homologous relationships.