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Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

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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: a growing plant comparative genomics resource.

Chengzhi Liang¹, Pankaj Jaiswal, Claire Hebbard

¹Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.

Nucleic Acids Research

|November 7, 2007

Summary

This summary is machine-generated.

Gramene provides comprehensive genetic and genomic data for major crops like rice and maize. This updated resource features new datasets, comparative genomics, and an improved interface for plant science research.

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Area of Science:

Plant genomics
Comparative genomics
Bioinformatics resources

Background:

Gramene is a curated resource for genetic, genomic, and comparative genomics data in plant species, particularly grasses.
It offers freely downloadable data and software for rice, maize, wheat, and other plant species.
Previous versions have established Gramene as a valuable tool for plant genetic research.

Purpose of the Study:

To update and expand the Gramene resource with new datasets and features.
To enhance data integration and provide new tools for plant genetic and evolutionary studies.
To improve the user interface for better accessibility and usability.

Main Methods:

Curating and integrating diverse genetic and genomic datasets, including genome assemblies, annotations, sequences, maps, genes, QTLs, and proteins.
Developing new features such as rice pathways, genetic diversity data, and large-scale genome comparisons.
Creating orthologous gene sets and phylogenetic trees across multiple plant and animal species.
Improving the web interface with a new navigation system, unified data pages, and enhanced search functionalities.

Main Results:

Inclusion of new datasets and enhanced connections among existing data types.
Introduction of rice pathways for functional gene annotation.
Availability of genetic diversity data for rice, maize, and wheat.
Implementation of large-scale genome comparisons and orthologous gene set creation.
Significant improvements to the web interface for a more user-friendly experience.

Conclusions:

The updated Gramene resource provides a more comprehensive and integrated platform for plant genetic and genomic research.
New features facilitate functional annotation, evolutionary studies, and analysis of genetic variation in crops.
Enhanced usability of the Gramene web interface supports broader accessibility for researchers worldwide.