Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex.

Autor:	Gout JF; Department of Biology, Indiana University, Bloomington, IN.; Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ.; Department of Biological Sciences, Mississippi State University, Starkville, MS., Hao Y; Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ.; Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ., Johri P; Department of Biology, Indiana University, Bloomington, IN.; Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ.; School of Life Sciences, Arizona State University, Tempe, AZ., Arnaiz O; Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France., Doak TG; Department of Biology, Indiana University, Bloomington, IN.; National Center for Genome Analysis Support, Indiana University, Bloomington, IN., Bhullar S; Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, Paris, France., Couloux A; Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Univ Evry, Université Paris-Saclay, Evry, France., Guérin F; Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France., Malinsky S; Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, Paris, France., Potekhin A; Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia.; Laboratory of Cellular and Molecular Protistology, Zoological Institute RAS, Saint Petersburg, Russia., Sawka N; Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Krakow, Poland., Sperling L; Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France., Labadie K; Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France., Meyer E; Institut de biologie de l'ENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, Paris, France., Duharcourt S; Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France., Lynch M; Department of Biology, Indiana University, Bloomington, IN.; Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ.
Jazyk:	angličtina
Zdroj:	Molecular biology and evolution [Mol Biol Evol] 2023 May 02; Vol. 40 (5).
DOI:	10.1093/molbev/msad107
Abstrakt:	Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD-derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance are still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the Paramecium aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and 1 additional out group, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene dosage changes. This exceptional data set of 13 species sharing an ancestral WGD and 2 closely related out group species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology. (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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