Published online 16 November 2006 Nucleic Acids Research, 2007, Vol. 35, Database issue D439–D444 doi:10.1093/nar/gkl777 ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data Olivier Arnaiz, Scott Cain1, Jean Cohen and Linda Sperling* Centre de Ge´ ne´ tique Mole´ culaire, CNRS, 91198 Gif-sur-Yvette, France and 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Received August 10, 2006; Revised September 27, 2006; Accepted September 29, 2006 ABSTRACT ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia. Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the Gif Paramecium stock collection. It is thus possible to navigate between sequences and stocks via the genes and alleles. Phenotypes, of mutant strains and of knockdowns obtained by RNA interference, are captured using controlled vocabularies according to the Entity-Attribute-Value model. ParameciumDB currently supports browsing of phenotypes, alleles and stocks as well as querying of sequence features (genes, UniProt matches, InterPro domains, Gene Ontology terms) and of genetic data (phenotypes, stocks, RNA interference experiments). Forms allow submission of RNA interference data and some bioinformatics services are available. Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community. A MODEL ORGANISM FOR THE 21ST CENTURY Paramecium is a unicellular eukaryote that belongs to the cili- ate phylum. Ciliates are the only unicellular organisms that separate germinal and somatic functions. Diploid but silent micronuclei undergo meiosis and transmit the genetic information to the next sexual generation. Highly polyploid macronuclei express the genetic information but develop anew at each sexual generation, through extensive pro- grammed rearrangements of the genome. Paramecium has long served as a model for the study of complex functions characteristic of multi-cellular organ- isms, including the somatic differentiation process (1), the biogenesis of cortical structures such as the ciliary basal bodies (2), regulated secretion (3), and receptor- and ion channel-mediated cell signaling in response to environmental stimuli (4,5). Standardized methods for Paramecium genetics have been available for half a century (6) and genes can be cloned by functional complementation (7). Over the past decade, gene silencing by somatic transformation (8) and RNA interference (RNAi) by feeding with bacteria that produce double-stranded RNA (9) have become routine laboratory procedures. Paramecium is a privileged model for investigation of non- Mendelian heredity and the underlying epigenetic mecha- nisms. Sonneborn (10) was the ﬁrst to document cytoplasmic heredity of mating type and other traits in Paramecium. It is just now becoming clear that these examples of cytoplas- mic heredity can be explained by homology-dependent mechanisms that involve non-coding RNA. The mechanisms, related to RNA interference and largely conserved among eukaryotes, enable comparison of the maternal somatic gen- ome with the zygotic genome by base pairing at the time of sexual processes. This comparison allows the maternal rear- rangement pattern to be transmitted to the new somatic nucleus (11). A second phenomenon, the cytoplasmic hered- ity of cortical pattern (12), is related to prion heredity. Corti- cal heredity also turns out to involve mechanisms that probably operate in all cells, to relay memory of cell shape through template-guided assembly of new structures in a pre-existing cellular space (13). The Paramecium tetraurelia macronuclear genome was sequenced by a whole genome shotgun approach at the Genoscope French National Sequencing Center, allowing discovery of nearly 40 000 protein-coding genes in the 72 Mb assembly. This unusually large number of genes, espe- cially for a unicellular organism, is the result of at least three successive whole genome duplications in the Paramecium lineage (14). The exceptional conservation of synteny between duplicated chromosomes, the high level of retention *To whom correspondence should be addressed. Tel: +33169823209; Fax: +33169823150; Email: sperling@cgm.cnrs-gif.fr 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.