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Jan 05, 2024;52 (D1): D1588-D1596.

PPGR: a comprehensive perennial plant genomes and regulation database.

Sen Yang, Wenting Zong, Lingling Shi, Ruisi Li, Zhenshu Ma, Shubao Ma, Jingna Si, Zhijing Wu, Jinglan Zhai, Yingke Ma, Zhuojing Fan, Sisi Chen, Huahong Huang, Deqiang Zhang, Yiming Bao, Rujiao Li, Jianbo Xie
Author Information
  1. Sen Yang: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  2. Wenting Zong: 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
  3. Lingling Shi: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  4. Ruisi Li: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  5. Zhenshu Ma: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  6. Shubao Ma: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  7. Jingna Si: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  8. Zhijing Wu: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  9. Jinglan Zhai: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  10. Yingke Ma: 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.
  11. Zhuojing Fan: 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. Sisi Chen: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
  13. Huahong Huang: State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
  14. Deqiang Zhang: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. ORCID
  15. Yiming Bao: 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. Rujiao Li: 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. Jianbo Xie: State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. ORCID
PMID: 37933857 DOI: 10.1093/nar/gkad963

Abstract

Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.cncb.ac.cn/ppgr/) to address this critical gap, by collecting, integrating, analyzing and visualizing genomic, gene regulation and functional data of perennial plants. PPGR currently includes 60 species, 847 million protein-protein/TF (transcription factor)-target interactions, 9016 transcriptome samples under various environmental conditions and genetic backgrounds. Noteworthy is the focus on genes that regulate wood production, seasonal dormancy, terpene biosynthesis and leaf senescence representing a wealth of information derived from experimental data, literature mining, public databases and genomic predictions. Furthermore, PPGR incorporates a range of multi-omics search and analysis tools to facilitate browsing and application of these extensive datasets. PPGR represents a comprehensive and high-quality resource for perennial plants, substantiated by an illustrative case study that demonstrates its capacity in unraveling gene functions and shedding light on potential regulatory processes.

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Grants

  1. QNTD202305/Central Universities
  2. 32371906/National Natural Science Foundation of China
  3. 2022YFD2201600/National Key R&D Program of China
  4. 2020132607/Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China
  5. XDB38030200/Chinese Academy of Sciences
  6. WX145XQ07-04/Genomics Data Center Construction of Chinese Academy of Sciences
  7. ANSO-PA-2020-07/Alliance of International Science Organizations
  8. /Open Biodiversity and Health Big Data Programme of IUBS

MeSH Term

Databases, Genetic
Genome, Plant
Genomics
Plants
Transcriptome
Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC009383 (PPGR)

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