pico‐PLAZA, a genome database of microbial photosynthetic eukaryotes

Summary With the advent of next generation genome sequenc- ing, 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 fami- lies, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining func- tional 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 func- tionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Func- tional 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 diver- sity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.