ArticleBMC genomics2010
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed, 74 citations in OpenAlex.
- The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.BMC biology · 2026Article
- Anthraquinone-2-Carboxylic Acid Is a Potential Antiviral Candidate Against Influenza Viruses In Vitro and In Vivo.Viruses · 2025Article
- CilioGenics: an integrated method and database for predicting novel ciliary genes.Nucleic acids research · 2024Article
- Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium.The EMBO journal · 2022Article
- The evolutionary conserved proteins CEP90, FOPNL, and OFD1 recruit centriolar distal appendage proteins to initiate their assembly.PLoS biology · 2022Article
- Ciliary Ca2+ pumps regulate intraciliary Ca2+ from the action potential and may co-localize with ciliary voltage-gated Ca2+ channels.The Journal of experimental biology · 2021Article
- Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx.Molecular & cellular proteomics : MCP · 2021Article
- MKS-NPHP module proteins control ciliary shedding at the transition zone.PLoS biology · 2020Article
- FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia.Molecular biology of the cell · 2019Article
- Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium.Nucleic acids research · 2019Article
- Motile Cilia: Innovation and Insight From Ciliate Model Organisms.Frontiers in cell and developmental biology · 2019Review
- A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium.Nucleic acids research · 2018Article
- C11orf70 Mutations Disrupting the Intraflagellar Transport-Dependent Assembly of Multiple Axonemal Dyneins Cause Primary Ciliary Dyskinesia.American journal of human genetics · 2018Article
- Transcriptional profiling of antioxidant defense system and heat shock protein (Hsp) families in the cadmium- and copper-exposed marine ciliate Euplotes crassu.Genes & genomics · 2018Article
- Two Sets of Piwi Proteins Are Involved in Distinct sRNA Pathways Leading to Elimination of Germline-Specific DNA.Cell reports · 2017Article
- Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.BMC genomics · 2017Article
- A meiosis-specific Spt5 homolog involved in non-coding transcription.Nucleic acids research · 2017Article
- Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies inMolecular biology of the cell · 2017Article
- Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids.G3 (Bethesda, Md.) · 2017Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsWe 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.
conclusionsA 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.