PlantTribes - Home 2.0

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With rapidly growing numbers of whole genome and expressed sequence tag (EST) sequences in our public databases, sequence-based protein classification systems are providing foundations for gene annotation, functional genomics, and comparative investigations of gene and genome evolution.

PlantTribes 2.0 is an objective classification system for plant proteins based on cluster analyses of the inferred proteomes of the sequenced angiosperms Arabidopsis thalliana v. Columbia (version 7), Carica papaya (version 1), Populus trichocarpa (version 1), Medicago truncatula (version 1), Oryza sativa (version 5), Sorghum bicolor (version 1), the lycophyte Selaginella moellendorffii (version 1), the moss Physcomitrella patens (version 1), and the green alga Chlamydomonas reinhardtii (version 3). You can search to identify genes by name, annotation, or find clusters containing your genes of interest. Once a gene or cluster has been identified, you can search for other related genes as members of the same group.

PlantTribes (Wall et al., 2008) is based on the similarity-based clustering procedure TribeMCL (Enright et al., 2002, 2003) to classify protein-coding genes into putative gene families. MCL classifications have been constructed using three clustering stringencies, allowing the user to explore the stability of the protein classification. A second round of MCL clustering based on the Tribe results identifies SuperTribes that approximate objective superfamilies. In PlantTribes 2.0, we have also added a 'finer scale' classification based on OrthoMCL (Li et al., 2003), in which gene clusters "orthogroups" are estimated that will ideally reflect the genes that have descended from a single ancestral gene in the study species. These are often narrower than Tribes, which are objective approximations of gene families. Finally, PlantTribes includes information about domains, traditional gene family names, and a unified nomenclature based on common terms.

Phylogenetic analyses of exemplar gene families show a strong, but not perfect correspondence between tribe membership and cladistic relationships. The results of these analyses provide insights into the Arabidopsis, Carica, Populus, Medicago, Oryza, Sorghum, Selaginella, Physcomitrella, and Chlamydomonas genomes, gene family evolution, and the evolutionary dynamics of functional domains among gene families. In addition, the resulting classification schemes provide scaffolds for sorting protein sequences from other plant species.

How to cite PlantTribes - We hope you find PlantTribes useful in your research and teaching. Please cite the following paper, which includes many technical details about the construction of the database and the user interface:

Wall, P.K., J. Leebens-Mack, K. Müller, D. Field, N. Altman and C.W. dePamphilis. (2008) PlantTribes: A gene and gene family resource for comparative genomics in plants. Nucleic Acids Research, 36:D970-976.

The original version of PlantTribes (1.0) is still available at Legacy PlantTribes. In addition to a searchable genome-based tribe scaffold based on early genome versions of Arabidopsis thaliana, Populus trichocharpa, Carica papaya, Medicago truncatula, and Oryza sativa PlantTribes 1.0 also incorporates an extensive collection of microarray expression data from Arabidopsis microarray experiments. Expression data is linked to the individual genes in PlantTribes, and can be accessed through any result including Arabidopsis gene sequences.

Please see the Documentation page for help and send comments, suggestions, questions, and/or bugs to Claude dePamphilis (cwd3 at psu dot edu) or Eric Wafula (ekw10 at psu dot edu).