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The PlantTribes database is a plant gene family database based on the …


Biology Articles » Botany » Plant Taxonomy » PlantTribes: a gene and gene family resource for comparative genomics in plants » Conclusions and future perspectives

Conclusions and future perspectives
- PlantTribes: a gene and gene family resource for comparative genomics in plants

 

The PlantTribes database offers a unique and powerful view of plant genomes and evolution. Collaborators working on annotation and interpretation of gene models for the Poplar and papaya genomes found the tribe results to be an invaluable tool for gene family identification and annotation, and our results were highlighted in the recent Poplar genome sequence paper (23). More than 15 other published articles to date have relied on data extracted from PlantTribes including expression divergence following gene duplication, identification of novel functional motifs, identification of gene families for intensive phylogenetic analysis and genome duplication history of basal angiosperms. With many plant genome sequence projects in progress, formal comparative approaches such as PlantTribes will allow researchers to rapidly identify the best gene models, quickly determine errors in the initial annotations, identify new gene families and increase the confidence in the limits and structure of existing gene families.

PlantTribes has been designed for ease of expansion and feature addition. As new genomes are sequenced, or large EST sets generated, PlantTribes will be continuously expanded to include these data. New features being developed presently include (i) a tool for the rapid incorporation of new query sequences into tribe alignments and phylogenies, (ii) connecting the rapidly expanding microRNA database into PlantTribes so that genes that are putative targets of known or predicted miRNAs may be easily found, (iii) expansion of the microarray database to include large-scale array experiments from basal angiosperms and other plants (26) that will facilitate cross-species expression analyses and (iv) synteny-based tools to map genome duplications onto gene-family phylogenies. As the number of sequenced genomes increases rapidly, the continued expansion of the PlantTribes database will facilitate a multitude of genome and gene-family studies, particularly homology-based annotation, genome-scale analysis of multiple gene families, characterization of large gene families and subsets of genes with common domain architectures.


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