PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

S. Proost, M. Van Bel, L. Sterck, K. Billiau, T. Van Parys, Y. Van de Peer, K. Vandepoele
2009 The Plant Cell  
Estimated number of pages : 15.5 The authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) are: Klaas Vandepoele (Klaas.Vandepoele@psb.vib-ugent.be) and Sebastian Proost (Sebastian.Proost@psb.vib-ugent.be). Abstract The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis
more » ... s significantly altered our view on the complexity of genome organization, gene function and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intra-species whole-genome dotplots and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive web interface. In addition, detailed documentation and tutorials introduce the different tools while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage. Allen, B.S., Stein, J.L., Stein, G.S., and Ostrer, H. (1991). Single-copy flanking sequences in human histone gene clusters map to chromosomes 1 and 6. Genomics 10, 486-488.
doi:10.1105/tpc.109.071506 pmid:20040540 pmcid:PMC2814516 fatcat:aojc3qdqnjgq3lwwivu67zixdy