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PTGBase: an integrated database to study tandem duplicated genes in plants
Jingyin Yu1, Tao Ke1, Sadia Tehrim1
1The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China and Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang 473061, China.
PTGBase is the first database for plant tandem duplicated genes, offering a comprehensive resource for 39 plant genomes. It provides detailed information on over 54,000 tandem duplicated gene clusters, aiding evolutionary and adaptation studies.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Tandem duplication is a common phenomenon in plant genomes, influencing gene family expansion, gene dosage, and adaptation.
- Previous research has identified numerous tandem duplication events, but a centralized, comprehensive database for plant kingdom-wide data was lacking.
Purpose of the Study:
- To develop the first comprehensive database, PTGBase, for plant tandem duplicated genes.
- To systematically integrate and present information on tandem duplicated genes across a wide range of plant species.
Main Methods:
- Compiled data from 39 plant genomes, including model and newly sequenced species.
- Developed a database (PTGBase) to store and characterize tandem duplicated gene clusters and their member genes.
- Implemented search and browsing functionalities based on identifiers, functional annotations, and sequence similarity.
Main Results:
- PTGBase contains 54,130 tandem duplicated gene clusters, encompassing 129,652 genes.
- Detailed characterization of each tandem array and its constituent genes is provided.
- Users can download data at various scales, from individual arrays to entire genome annotations.
Conclusions:
- PTGBase serves as a valuable and comprehensive resource for studying plant tandem duplicated genes.
- The database facilitates research into the evolutionary and adaptive roles of tandem duplications in plants.
- Future updates will incorporate data from newly sequenced plant species.
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