Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM et al.. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178

Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France.
Nature (Impact Factor: 41.46). 12/2006; 444(7116):171-8. DOI: 10.1038/nature05230
Source: PubMed


The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.

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Available from: Sandra Duharcourt, Oct 09, 2015
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    • "Over the last ten years, high throughput sequencing has made ciliate genomic research available on a large scale, and the genomes of several species have been sequenced and analyzed, e.g. Tetrahymena thermophila (Eisen et al., 2006), Paramecium tetraurelia (Auryet al., 2006), Ichthyophthirius multifiliis (Coyne et al., 2011) and Oxytricha trifallax (Swart et al., 2013). "
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    • "The MIC genome has been a mysterious puzzle, harboring not only a labyrinth of hundreds of thousands of intricately organized gene segments but also other germline-limited elements that could be involved in genome rearrangement. High quality draft somatic genome sequences have been reported for the main model ciliates Tetrahymena (Eisen et al., 2006), Paramecium (Aury et al., 2006), and Oxytricha (Swart et al., 2013). Although genome-wide IES studies have been reported for Paramecium and Tetrahymena (Arnaiz et al., 2012; Fass et al., 2011), neither of which has scrambled genes, no comprehensive germline genome has been described to date for any ciliate species, nor for any organism with a scrambled genome. "
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    • "November 26, 2013, possessing the Pfam core histone domain). Likely as a consequence of multiple whole-genome duplications (Aury et al. 2006), the record holder for histone variants among ciliates is Paramecium tetraurelia, with 30 distinct histone variants (histone H4: 5, histone H3: 10; histone H2B: 6, and histone H2A: 9). For the purposes of comparison, we found 48 distinct human histone variants in UniProt (December 1, 2013). "
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