PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants (original) (raw)

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Sebastian Proost ,

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Michiel Van Bel ,

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Lieven Sterck ,

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Kenny Billiau ,

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Thomas Van Parys ,

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Yves Van de Peer ,

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Klaas Vandepoele

aDepartment of Plant Systems Biology, Flanders Institute for Biotechnology, B-9052 Ghent, Belgium

bDepartment of Molecular Genetics, Ghent University, B-9052 Ghent, Belgium

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Received:

22 September 2009

Revision received:

04 December 2009

Accepted:

10 December 2009

Published:

29 December 2009

Cite

Sebastian Proost, Michiel Van Bel, Lieven Sterck, Kenny Billiau, Thomas Van Parys, Yves Van de Peer, Klaas Vandepoele, PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants, The Plant Cell, Volume 21, Issue 12, December 2009, Pages 3718–3731, https://doi.org/10.1105/tpc.109.071506
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Abstract

The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has 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, intraspecies whole-genome dot plots, 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.

© 2009 American Society of Plant Biologists

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