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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Published on: June 17, 2012

Gramene 2013: comparative plant genomics resources.

Marcela K Monaco¹, Joshua Stein, Sushma Naithani

¹Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA.

Nucleic Acids Research

|November 13, 2013

Summary

This summary is machine-generated.

Gramene is a comprehensive online resource for plant comparative genomics, offering integrated data and tools for exploring crop and model species genomes. It supports research in plant evolution, genetics, and breeding through phylogenetic analysis and pathway databases.

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Area of Science:

Plant Genomics
Comparative Genomics
Bioinformatics

Background:

Gramene is a curated online resource for comparative functional genomics in crops and model plant species.
It hosts 27 fully and 10 partially sequenced reference genomes.
Its strength lies in applying a phylogenetic framework and ontologies for genome comparison and data integration.

Purpose of the Study:

To provide a robust platform for comparative functional genomics research in plants.
To integrate structural and functional annotation data using ontologies.
To support scientific research in plant evolution, genetics, breeding, and systems biology.

Main Methods:

Whole-genome alignments and phylogenetic gene family trees for inferring relationships.
Integration of genetic variation data, sequences, and genome mappings.
Development and hosting of species-specific metabolic pathway databases using Pathway Tools software.

Main Results:

Hosting of 27 fully and 10 partially sequenced reference genomes.
Availability of genetic variation data, sequences, and genome mappings for 10 species.
Inclusion of 10 species-specific metabolic pathway databases and a Plant Reactome portal for rice.

Conclusions:

Gramene serves as a unique community platform for plant genomics research.
The resource facilitates studies in evolution, genetics, breeding, molecular biology, biochemistry, and systems biology.
Expansion of the Plant Reactome portal to include more plant species is planned.