PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants

Abstract

PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads. In this latest release of the PLAZA platform, we are integrating a record number of 134 high-quality plant genomes, split up over two instances: PLAZA Dicots 5.0 and PLAZA Monocots 5.0. This number of genomes corresponds with a massive expansion in the number of available species when compared to PLAZA 4.0, which offered access to 71 species, a 89% overall increase. The PLAZA 5.0 release contains information for 5 882 730 genes, and offers pre-computed gene families and phylogenetic trees for 5 274 684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website: https://bioinformatics.psb.ugent.be/plaza/.

Figure 1.

Species overview PLAZA 5.0. Overview of the species (yellow bars), taxonomic families (blue bars), and taxonomic orders (leaf nodes in the tree) in PLAZA 5.0 offset against the same content types in PLAZA 4.0. Bars that are solely to the left of the center indicate that there is no increase in PLAZA 5.0, while bars that are solely to the right of the center indicate that this order was not previously present in PLAZA 4.0. Bars with content to both sides of the center indicate that the order has been extended by the addition of new species and/or families in PLAZA 5.0.

Figure 2.

BED import and improved functional enrichment visualization. (A) After selecting the target species and gene types to be included (Zea mays B73, NAM v5.0), and uploading an example BED file (maize GLK2 ChIP-Seq (26)), each region is associated to the closest gene. Next, an interactive peak-to-gene distance distribution for all peaks and their associated closest genes is shown. A distance cutoff can be applied to retain all genes, or only regions overlapping with the gene body, or within a predefined distance to the closest gene. Applying a 2 kb cutoff retained 3758 genes in this workbench experiment. (B) Overview of a GO enrichment analysis for maize GLK2 ChIP-Seq target genes. Through the Graph visualization, the Filtered view discards parental GO terms and reports the most specific GO terms showing significant enrichment. While node size is proportional to the P-value of the enriched term, the node color is determined by the enrichment fold of the ontology term, with the color scale varying between green and purple (high and low values, depicting over-representation and depletion, respectively). The node outer band is determined by the percentage of genes that are annotated with the enriched ontology term (e.g. the selected node GO:0015979 reports that 2.50% of the genes in this workbench experiment are annotated with the enriched GO Biological Process term photosynthesis).