PLAZA 3.0: an access point for plant comparative genomics

Abstract

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.

Figure 1.

Gene page in PLAZA 3.0. From top to bottom, (A) the header with the menu and search functions, (B) the general information (links to the gene family, alternative gene names or identifiers) and Descriptions for gene AT1G01720, (C) the toolbox that allows different actions to be performed, (D) tabs with detailed functional information and (E) the footer with links to general information. A similar layout is consistently used on all pages describing different data types.

Figure 2.

Overview of the number of genes and genomes in the different PLAZA versions. The bar chart (values on the left-axis) indicates the number of genes present in the different PLAZA versions. The superimposed line charts (percentages on the right-axis) denote the percentage of genes present in a gene family or having GO functional annotation. For each version, the number of integrated genomes is shown in parenthesis. Note that there are 10 shared species in PLAZA 3.0 dicots and monocots (Supplementary Table S1).

Figure 3.

Fractions of genes in Gramene (release 41), PLAZA 2.5 and PLAZA 3.0 dicots with a description and a GO Biological Process annotation for five selected species (Arabidopsis thaliana, Brassica rapa, Glycine max, Solanum lycopersicum and Zea mays). Blue indicates the fraction with a description or primary GO label (derived from the GO consortium, UniProtKB/Swiss-Prot or InterProScan), green the fraction with a projected GO label only and gray the fraction without description/GO.