Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

By J. Aury, O. Jaillon, L. Duret, B. Noel, Claire Jubin, Betina M. Porcel, Béatrice Segurens, V. Daubin, Véronique Anthouard, N. Aiach and 33 more. Nature, 2006

845 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/006a88e73c63b05133af254f8d16a76f0942b594

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

The evolutionary significance of ancient genome duplications (2009, background): “More recently, it was shown that the unicellular ciliate Paramecium tetraurelia has also undergone several WGD”
Evolutionary genetics of genome merger and doubling in plants. (2008, background): “The finding that many gene functional groups show convergent patterns of retention or loss following independent duplications that are separated by hundreds of millions of years of evolution (81) is supported by postduplication convergence of gene copy number in divergent yeasts (92), and by the fin”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, background): “…nucleotide substitution per synonymous site (Ks) between paleolog pairs (syntenic paralogs), filtering out the inevitable influence of background (i.e., single gene) duplications, which superimpose an L-shaped curve on the relics of whole-genome duplications (Blanc and Wolfe 2004; Cui et al. 2006).”
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing (2014, background): “In other cases, they provide genomic data from a diverse selection of taxa within a lineage where only sparse genomic data previously existed from a few distant relatives (such as the ciliates [18–20]).”
PGDD: a database of gene and genome duplication in plants (2012, background): “Although new data from yeast (15–17) and Paramecium (18) are shedding valuable light on consequences of GD in microbes, these consequences are expected to be very different in organisms with small effective population sizes such as angiosperms, mammals and other higher eukaryotes (19,20).”