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

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Published on: June 17, 2012

GreenPhylDB v2.0: comparative and functional genomics in plants.

Mathieu Rouard¹, Valentin Guignon, Christelle Aluome

¹Bioversity International - CfL programme Parc Scientifique Agropolis II, 34397 Montpellier, France. m.rouard@cgiar.org

Nucleic Acids Research

|September 25, 2010

Summary

This summary is machine-generated.

GreenPhylDB version 2 offers a comprehensive resource for plant comparative genomics, featuring 16 plantae kingdom genomes clustered into gene families for evolutionary analysis and gene discovery.

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Area of Science:

Bioinformatics
Genomics
Evolutionary Biology

Background:

Comparative genomics facilitates understanding of evolutionary processes and gene function.
Databases are crucial for organizing and accessing large-scale genomic data.
Plant genomics research requires integrated resources for analyzing gene families across diverse species.

Purpose of the Study:

To present GreenPhylDB version 2, an updated database for comparative and functional genomics of plantae.
To provide enhanced tools and data for analyzing gene families and orthologous relationships.
To facilitate gene discovery and evolutionary insights within a broad taxonomic context.

Main Methods:

Integration of 16 complete plantae kingdom genomes.
Automatic clustering of genes into families.
Manual annotation and phylogenetic analysis of gene families.
Development of improved web interfaces and analysis tools, including an ontology browser.

Main Results:

GreenPhylDB v2 contains 16 plantae genomes, from algae to angiosperms.
Gene families are automatically clustered and manually annotated.
Phylogenetic analysis elucidates orthologous and paralogous relationships.
Provides access to gene composition, protein domains, publications, and ortholog predictions.
Enhanced navigation and new analysis tools, including a gene family ontology browser.

Conclusions:

GreenPhylDB v2 is a valuable resource for plant comparative genomics.
The database aids in understanding evolutionary processes through gene family analysis.
Facilitates accelerated gene discovery in plants.
Enhances exploration of gene families across a wide taxonomic range.