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Updated: Jun 8, 2026

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

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

Published on: June 17, 2012

Gramene database: a hub for comparative plant genomics.

Pankaj Jaiswal¹

¹Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.

Methods in Molecular Biology (Clifton, N.J.)

|October 9, 2010

Summary

This summary is machine-generated.

Gramene is a powerful database integrating diverse plant genomic data for cereals and model plants. It aids researchers in exploring gene functions and interactions to understand plant development and agronomic traits.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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Area of Science:

Genomics
Bioinformatics
Plant Biology

Background:

The completion of the rice genome sequencing project and existing genetic information offer tools for studying plant agronomic traits.
Genomic colinearity and comparative genomics are crucial for understanding plant genomes.
Databases are essential for integrating and exploring vast amounts of genetic and genomic data.

Purpose of the Study:

To introduce Gramene, a comprehensive database for plant genomic studies.
To highlight Gramene's utility in exploring genomic colinearity and comparative genomics.
To demonstrate how Gramene facilitates research across various plant science disciplines.

Main Methods:

Assimilation of publicly available data from diverse cereal crops (rice, sorghum, maize, etc.), grape, poplar, and Arabidopsis.
Reanalysis and integration of data into knowledge domains including maps, markers, genes, proteins, pathways, phenotypes, Quantitative Trait Loci (QTL), and genetic diversity.
Utilizing genomic colinearity and comparative genomics for data exploration.

Main Results:

Gramene provides a unified platform for accessing and analyzing integrated genomic data for multiple plant species.
The database enables researchers to investigate gene roles, genomic organization, and interactions regulating plant development.
Examples from rice illustrate the database's application in diverse research areas.

Conclusions:

Gramene serves as a valuable resource for researchers in plant biology, breeding, genomics, and related fields.
The database facilitates deciphering interactions within biological systems and their role in plant development.
Comparative genomics and integrated data analysis through Gramene advance our understanding of plant agronomic traits.