National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D1651-D1660. doi: 10.1093/nar/gkad870.
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 rapid development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amount of data, which urgently needs an effective platform for data integration and sharing. However, the existing databases cannot fully satisfy researchers' requirements due to the relatively limited integration level and untimely update. Here, we present the Tropical Crop Omics Database (TCOD, https://ngdc.cncb.ac.cn/tcod), a comprehensive multi-omics data platform for tropical crops. TCOD integrates diverse omics data from 15 species, encompassing 34 chromosome-level de novo assemblies, 1 255 004 genes with functional annotations, 282 436 992 unique variants from 2048 WGS samples, 88 transcriptomic profiles from 1997 RNA-Seq samples and 13 381 germplasm items. Additionally, TCOD not only employs genes as a bridge to interconnect multi-omics data, enabling cross-species comparisons based on homology relationships, but also offers user-friendly online tools for efficient data mining and visualization. In short, TCOD integrates multi-species, multi-omics data and online tools, which will facilitate the research on genomic selective breeding and trait biology of tropical crops.
热带作物对热带农业至关重要，资源稀缺、功能多样且市场需求广泛，为世界热带农业生产国带来了可观的经济效益。测序技术的快速发展推动了热带作物研究的一个里程碑，产生了大量的数据，这些数据迫切需要一个有效的平台进行数据集成和共享。然而，由于整合水平相对有限且更新不及时，现有的数据库无法完全满足研究人员的需求。在这里，我们介绍了热带作物组学数据库（TCOD，https://ngdc.cncb.ac.cn/tcod），这是一个用于热带作物的综合性多组学数据平台。TCOD 整合了来自 15 个物种的多种组学数据，包括 34 个染色体水平的从头组装、1255004 个具有功能注释的基因、2048 个 WGS 样本中的 282436992 个独特变体、1997 个 RNA-Seq 样本中的 88 个转录组图谱和 13381 个种质项目。此外，TCOD 不仅使用基因作为连接多组学数据的桥梁，实现基于同源关系的跨物种比较，还提供了用户友好的在线工具，用于高效的数据挖掘和可视化。总之，TCOD 整合了多物种、多组学数据和在线工具，将促进热带作物基因组选择育种和性状生物学的研究。
