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Updated: Mar 30, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
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Gramene 2016: comparative plant genomics and pathway resources
Marcela K Tello-Ruiz1, Joshua Stein1, Sharon Wei1
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Nucleic Acids Research
|November 11, 2015
Summary
Gramene provides an updated online resource for comparative functional genomics in crops and model plants. It integrates 39 reference genomes and plant pathways, enhancing access to genetic variation and expression data.
Area of Science:
- Plant genomics
- Comparative genomics
- Functional genomics
Background:
- Gramene is a key online resource for comparative functional genomics in plants.
- The platform integrates genome and pathway data for crops and model species.
- Previous versions have provided valuable comparative maps, markers, and quantitative trait loci (QTL).
Purpose of the Study:
- To update users on the latest enhancements to the Gramene resource.
- To highlight the integration of new data types and improved accessibility.
- To showcase new educational resources for users.
Main Methods:
- Utilizing a new Drupal management platform for the website.
- Integrating 39 fully assembled reference genomes with ontology-based annotation.
- Developing the Plant Reactome pathway portal with curated and projected pathways.
- Interfacing genome and pathway browsers with EMBL-EBI's Expression Atlas.
Main Results:
- The Gramene genomes section now features 39 reference genomes with integrated annotation and comparative analyses.
- The Plant Reactome portal offers curated rice pathways and homology-based projections for 33 species.
- Expression data from curated studies is accessible through integrated browsers.
- An archive website maintains access to legacy data, complemented by new educational webinars and tutorials.
Conclusions:
- Gramene continues to be a vital, evolving resource for plant comparative genomics.
- Enhanced data integration and accessibility facilitate deeper biological insights.
- New educational initiatives broaden user engagement and understanding of plant genomics.
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