PLAZA 3.0: an access point for plant comparative genomics.

Sebastian Proost,Yves Van De Peer,Michiel Van Bel,Klaas Vandepoele,Dries Vaneechoutte,Bernd Mueller-Roeber,Dirk Inzé

doi:10.1093/nar/gku986

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.

Highlights

Since the introduction of generation sequencing technologies, the price for sequencing a new genome has dropped considerably
The extraction of biological knowledge from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species, is an important concept. By using such comparative approaches, (i) knowledge can be transferred from model to non-model organisms [2], (ii) insights can be gained in the evolution of specific genes or entire metabolic and signaling pathways [3], (iii) genes of importance for niche-specific plant adaptations can be identified [4] and (iv) large-scale genomic events, such as whole-genome duplications (WGDs), can be unveiled [5]
We present version 3.0 of PLAZA, an online resource that offers comparative genomics data for 37 plant species (Supplementary Table S1) and allows users to browse the annotated genomes, gene families and phylogenetic trees

Summary

Introduction

Since the introduction of generation sequencing technologies, the price for sequencing a new genome has dropped considerably. 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.

Results

Conclusion