PIECE 2.0: an update for the plant gene structure comparison and evolution database.
Yi Wang1,2,3, Ling Xu2,3, Roger Thilmony1
1USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.
Nucleic Acids Research
|October 16, 2016
Summary
The updated PIECE 2.0 database now includes intron and exon information for plant genes from 49 species. This resource aids in comparing gene structure and understanding plant genome evolution.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- The PIECE database provides plant gene intron-exon organization data.
- Understanding gene structure evolution is crucial for plant biology.
Purpose of the Study:
- To announce the release and features of PIECE 2.0, an updated database for plant gene structure analysis.
- To enhance comparative genomics and evolutionary studies in plants.
Main Methods:
- Database update with expanded species coverage (49 plant species).
- Integration of new features: phylogenetic tree viewer, gene grouping by KOG/KO/Pfam, inclusion of intronless genes.
- Implementation of an improved GSDraw tool for gene structure visualization.
Main Results:
- PIECE 2.0 now contains annotated genes from 49 plant species, significantly expanding comparative capabilities.
- New visualization and grouping tools facilitate detailed analysis of gene structure and phylogenetic relationships.
- Statistical summaries enable cross-species comparisons of gene structure patterns.
Conclusions:
- PIECE 2.0 is a significantly enhanced resource for plant researchers studying gene structure and evolution.
- The expanded data and improved tools will advance comparative genomics and evolutionary insights in plants.
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