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ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.

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.

SUBMITTER: Arnaiz O

PROVIDER: S-EPMC1669747 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND: The genome of Paramecium tetraurelia, a unicellular model that belongs to the ciliate phylum, has been shaped by at least 3 successive whole genome duplications (WGD). These dramatic events, which have also been documented in plants, animals and fungi, are resolved over evolutionary time by the loss of one duplicate for the majority of genes. Thanks to a low rate of large scale genome rearrangement in Paramecium, an unprecedented large number of gene duplicates of different ages have been identified, making this organism an outstanding model to investigate the evolutionary consequences of polyploidization. The most recent WGD, with 51% of pre-duplication genes still in 2 copies, provides a snapshot of a phase of rapid gene loss that is not accessible in more ancient polyploids such as yeast. RESULTS: We designed a custom oligonucleotide microarray platform for P. tetraurelia genome-wide expression profiling and used the platform to measure gene expression during 1) the sexual cycle of autogamy, 2) growth of new cilia in response to deciliation and 3) biogenesis of secretory granules after massive exocytosis. Genes that are differentially expressed during these time course experiments have expression patterns consistent with a very low rate of subfunctionalization (partition of ancestral functions between duplicated genes) in particular since the most recent polyploidization event. CONCLUSIONS: A public transcriptome resource is now available for Paramecium tetraurelia. The resource has been integrated into the ParameciumDB model organism database, providing searchable access to the data. The microarray platform, freely available through NimbleGen Systems, provides a robust, cost-effective approach for genome-wide expression profiling in P. tetraurelia. The expression data support previous studies showing that at short evolutionary times after a whole genome duplication, gene dosage balance constraints and not functional change are the major determinants of gene retention.

Project description:BackgroundA Paramecium tetraurelia pilot genome project, the subsequent sequencing of a Megabase chromosome as well as the Paramecium genome project aimed at gaining insight into the genome of Paramecium. These cells display a most elaborate membrane trafficking system, with distinct, predictable pathways in which actin could participate. Previously we had localized actin in Paramecium; however, none of the efforts so far could proof the occurrence of actin in the cleavage furrow of a dividing cell, despite the fact that actin is unequivocally involved in cell division. This gave a first hint that Paramecium may possess actin isoforms with unusual characteristics. The genome project gave us the chance to search the whole Paramecium genome, and, thus, to identify and characterize probably all actin isoforms in Paramecium.ResultsThe ciliated protozoan, P. tetraurelia, contains an actin multigene family with at least 30 members encoding actin, actin-related and actin-like proteins. They group into twelve subfamilies; a large subfamily with 10 genes, seven pairs and one trio with > 82% amino acid identity, as well as three single genes. The different subfamilies are very distinct from each other. In comparison to actins in other organisms, P. tetraurelia actins are highly divergent, with identities topping 80% and falling to 30%. We analyzed their structure on nucleotide level regarding the number and position of introns. On amino acid level, we scanned the sequences for the presence of actin consensus regions, for amino acids of the intermonomer interface in filaments, for residues contributing to ATP binding, and for known binding sites for myosin and actin-specific drugs. Several of those characteristics are lacking in several subfamilies. The divergence of P. tetraurelia actins and actin-related proteins between different P. tetraurelia subfamilies as well as with sequences of other organisms is well represented in a phylogenetic tree, where P. tetraurelia sequences only partially cluster.ConclusionAnalysis of different features on nucleotide and amino acid level revealed striking differences in isoforms of actin and actin-related proteins in P. tetraurelia, both within the organism and in comparison to other organisms. This diversification suggests unprecedented specification in localization and function within a unicellular eukaryote.

Dataset Information

ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.

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