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PlantPan: A comprehensive multi-species plant pan-genome database
Meiye Jiang1,2,3, Qiheng Qian1,2,3, Mingming Lu1,2,3
1National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China.
The Plant Journal : for Cell and Molecular Biology
|April 12, 2025
Summary
PlantPan is a new database integrating multi-species plant pan-genome analysis, offering comprehensive genomic diversity data for crop improvement and evolutionary studies. It provides gene, sequence, and variation information across 11 species.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- The pan-genome, representing complete genomic diversity, is crucial for studying plant evolution, domestication, and breeding.
- Existing single-species plant pan-genome databases are limited, and multi-species resources are scarce.
- Inconsistent analysis methods across databases hinder comparative pan-genome studies.
Purpose of the Study:
- To develop PlantPan, a comprehensive multi-species plant pan-genome database.
- To standardize and integrate pan-genome analysis results for 11 plant species.
- To facilitate research in plant evolution, crop domestication, and breeding.
Main Methods:
- Compiled pan-genome analysis results for 195 genomes from 11 plant species.
- Integrated gene-centric, sequence-centric, and graph-based pan-genome data.
- Included data on pan-genome openness, gene functions, variations, homologous genes, and gene clusters.
Main Results:
- PlantPan houses over 9 million genes, 694,000 gene clusters, and 526 million genome variations.
- The database contains extensive functional gene information, including transcription factors, resistance genes, and pathway-related genes.
- It provides 33 million genome synteny entries and 177,000 non-redundant synteny groups.
Conclusions:
- PlantPan serves as a vital, integrated platform for multi-species plant pan-genome research.
- The database supports advancements in crop molecular breeding and plant evolutionary studies.
- It addresses the need for standardized, comparative pan-genome data across diverse plant species.
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