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 wellcharacterized
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.
