Gene expression in a paleopolyploid: a transcriptome resource for the ciliate <i>Paramecium tetraurelia</i>

作     者：Arnaiz, Olivier Gout, Jean-Francois Betermier, Mireille Bouhouche, Khaled Cohen, Jean Duret, Laurent Kapusta, Aurelie Meyer, Eric Sperling, Linda 

作者机构：Univ Paris Sud Ctr Genet Mol CNRS FRE3144 Gif Sur Yvette France Univ Lyon 1 CNRS UMR 5558 Lab Biometrie & Biol Evolut F-69622 Villeurbanne France Ecole Normale Super CNRS Inst Biol INSERMUMR8197U1024 Paris France Indiana Univ Dept Biol Bloomington IN 47405 USA 

出 版 物：《BMC GENOMICS》 (BMC基因)

年 卷 期：2010年第11卷第1期

页      面：547-547页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 0836[工学-生物工程] 

基　　金：ANR (Agence National de la Recherche) [ANR-08-BLAN-0233] CNRS (Centre National de la Recherche Scientifique) Equipe FRM (Fondation de la Recherche Medicale) French Ministry of Higher Education and Research FRM Agence Nationale de la Recherche (ANR) [ANR-08-BLAN-0233] Funding Source: Agence Nationale de la Recherche (ANR) 

主　　题：Microarray Platform Whole Genome Duplication Gene Retention Limma Package Whole Genome Duplication Event 

摘      要：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