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Jan 05, 2024;52 (D1): D1651-D1660.

TCOD: an integrated resource for tropical crops.

Hailong Kang, Tianhao Huang, Guangya Duan, Yuyan Meng, Xiaoning Chen, Shuang He, Zhiqiang Xia, Xincheng Zhou, Jinquan Chao, Bixia Tang, Zhonghuang Wang, Junwei Zhu, Zhenglin Du, Yanlin Sun, Sisi Zhang, Jingfa Xiao, Weimin Tian, Wenquan Wang, Wenming Zhao
Author Information
  1. Hailong Kang: 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.
  2. Tianhao Huang: 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.
  3. Guangya Duan: 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. ORCID
  4. Yuyan Meng: 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.
  5. Xiaoning Chen: 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.
  6. Shuang He: Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China.
  7. Zhiqiang Xia: Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China. ORCID
  8. Xincheng Zhou: Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
  9. Jinquan Chao: Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
  10. Bixia Tang: 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. ORCID
  11. Zhonghuang Wang: 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.
  12. Junwei Zhu: 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. ORCID
  13. Zhenglin Du: 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.
  14. Yanlin Sun: 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. ORCID
  15. Sisi Zhang: 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.
  16. Jingfa Xiao: 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. ORCID
  17. Weimin Tian: Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
  18. Wenquan Wang: Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China.
  19. Wenming Zhao: 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.
PMID: 37843152 DOI: 10.1093/nar/gkad870

Abstract

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.

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Grants

  1. 2018YFD1000505/National Key R&D Program of China
  2. XDB38050300/Strategic Priority Research Program of the Chinese Academy of Sciences
  3. 32100506/National Natural Science Foundation of China
  4. CAS-WX2022SDC-XK05/Genomics Data Center Operation and Maintenance of Chinese Academy of Sciences
  5. B21HJ0001/Developing Bioinformatics Platform in Hainan Yazhou Bay Seed Lab

MeSH Term

Crops, Agricultural
Databases, Genetic
Transcriptome
Genome, Plant
Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC008232 (TCOD)

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