title: pico-PLAZA, a genome database of microbial photosynthetic eukaryotes.
abstract: With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium. klaas.vandepoele@psb.vib-ugent.be
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
authors.forename: Michiel
authors.initials: M
authors.lastname: Van Bel
authors.forename: Guilhem
authors.initials: G
authors.lastname: Richard
authors.forename: Sofie
authors.initials: S
authors.lastname: Van Landeghem
authors.forename: Bram
authors.initials: B
authors.lastname: Verhelst
authors.forename: Hervé
authors.initials: H
authors.lastname: Moreau
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Nigel
authors.initials: N
authors.lastname: Grimsley
authors.forename: Gwenael
authors.initials: G
authors.lastname: Piganeau
mesh_terms: D000460:Chlorophyta / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D030541:Databases, Genetic / Q000592:standards* / Q000639:trends*; D017377:Diatoms / Q000235:genetics; D056890:Eukaryota / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics