title: Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
abstract: 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.
authors.affiliation: Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.forename: Laurent
authors.initials: L
authors.lastname: Duret
authors.forename: Benjamin
authors.initials: B
authors.lastname: Noel
authors.forename: Claire
authors.initials: C
authors.lastname: Jubin
authors.forename: Betina M
authors.initials: BM
authors.lastname: Porcel
authors.forename: Béatrice
authors.initials: B
authors.lastname: Ségurens
authors.forename: Vincent
authors.initials: V
authors.lastname: Daubin
authors.forename: Véronique
authors.initials: V
authors.lastname: Anthouard
authors.forename: Nathalie
authors.initials: N
authors.lastname: Aiach
authors.forename: Olivier
authors.initials: O
authors.lastname: Arnaiz
authors.forename: Alain
authors.initials: A
authors.lastname: Billaut
authors.forename: Janine
authors.initials: J
authors.lastname: Beisson
authors.forename: Isabelle
authors.initials: I
authors.lastname: Blanc
authors.forename: Khaled
authors.initials: K
authors.lastname: Bouhouche
authors.forename: Francisco
authors.initials: F
authors.lastname: Câmara
authors.forename: Sandra
authors.initials: S
authors.lastname: Duharcourt
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigo
authors.forename: Delphine
authors.initials: D
authors.lastname: Gogendeau
authors.forename: Michael
authors.initials: M
authors.lastname: Katinka
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Keller
authors.forename: Roland
authors.initials: R
authors.lastname: Kissmehl
authors.forename: Catherine
authors.initials: C
authors.lastname: Klotz
authors.forename: France
authors.initials: F
authors.lastname: Koll
authors.forename: Anne
authors.initials: A
authors.lastname: Le Mouël
authors.forename: Gersende
authors.initials: G
authors.lastname: Lepère
authors.forename: Sophie
authors.initials: S
authors.lastname: Malinsky
authors.forename: Mariusz
authors.initials: M
authors.lastname: Nowacki
authors.forename: Jacek K
authors.initials: JK
authors.lastname: Nowak
authors.forename: Helmut
authors.initials: H
authors.lastname: Plattner
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Françoise
authors.initials: F
authors.lastname: Ruiz
authors.forename: Vincent
authors.initials: V
authors.lastname: Serrano
authors.forename: Marek
authors.initials: M
authors.lastname: Zagulski
authors.forename: Philippe
authors.initials: P
authors.lastname: Dessen
authors.forename: Mireille
authors.initials: M
authors.lastname: Bétermier
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.forename: Claude
authors.initials: C
authors.lastname: Scarpelli
authors.forename: Vincent
authors.initials: V
authors.lastname: Schächter
authors.forename: Linda
authors.initials: L
authors.lastname: Sperling
authors.forename: Eric
authors.initials: E
authors.lastname: Meyer
authors.forename: Jean
authors.initials: J
authors.lastname: Cohen
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
mesh_terms: D000818:Animals; D005057:Eukaryotic Cells / Q000378:metabolism; D019143:Evolution, Molecular; D020440:Gene Duplication; D020131:Genes, Duplicate / Q000235:genetics; D017125:Genes, Protozoan / Q000235:genetics; D018503:Genome, Protozoan / Q000235:genetics*; D023281:Genomics; D008969:Molecular Sequence Data; D016805:Paramecium tetraurelia / Q000235:genetics*; D010802:Phylogeny