TCOD: an Integrated Resource for Tropical Crops
Tropical crops are vital for tropical agriculture, with resource scarcity, functional diversity and extensive market demand, providing considerable economic benefits for the world's tropical agriculture-producing countries. The expeditious development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amounts of data. However, the scattered nature of this data across various centers and websites presents an inconvenience for scientific researchers in utilization, highlighting the urgent need for establishing a comprehensive data integration and sharing platform to facilitate convenient data retrieval and online analysis.
Recently, researchers led by ZHAO Wenming from the National Genomics Data Center, Beijing Institute of Genomics of Chinese Academy of Sciences (China National Center for Bioinformation) and WANG Wenquan from the Hainan University have jointly developed the Tropical Crop Omics Database (TCOD). This work was published online in Nucleic Acids Research with the title "TCOD: an integrated resource for tropical crops".
TCOD integrates diverse omics data from 15 species (such as cassava, rubber tree, coffee, cocoa, banana, etc.), encompassing 34 chromosome-level de novo assemblies, 1,255,004 genes with functional annotations, 282,436,992 unique variants from 2,048 WGS samples, 88 transcriptomic profiles from 1,997 RNA-Seq samples, and 13,381 germplasm items. TCOD employs genes as a bridge to interconnect multi-omics data, offering users a one-stop solution for data browsing, retrieval, and download. Additionally, it furnishes homologous gene relationships across genomes of diverse species, enabling in-depth exploration of shared biological characteristics by gene function, pathway annotation, genome variation, and gene expression, thereby promoting cross-species research. Moreover, to enhance effective data mining, TCOD offers a series of online tools for sequence similarity comparison, downstream primer design, literature searches, genes pathway enrichment, homologous gene discovery and pairwise genome consensus linear views.
In the era of Breeding 4.0 and the advancement of artificial intelligence technology, TCOD amalgamates multi-species, multi-omics data, and online tools to provide support for selective breeding and trait enhancement in tropical crops.
The construction pipelines of TCOD
Prof. ZHAO Wenming
Prof. WANG Wenquan