Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.
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.
Aury
Jean-Marc
JM
Genoscope and CNRS UMR 8030, 2 rue Gaston Crémieux CP5706, 91057 Evry, France.
Jaillon
Olivier
O
Duret
Laurent
L
Noel
Benjamin
B
Jubin
Claire
C
Porcel
Betina M
BM
Ségurens
Béatrice
B
Daubin
Vincent
V
Anthouard
Véronique
V
Aiach
Nathalie
N
Arnaiz
Olivier
O
Billaut
Alain
A
Beisson
Janine
J
Blanc
Isabelle
I
Bouhouche
Khaled
K
Câmara
Francisco
F
Duharcourt
Sandra
S
Guigo
Roderic
R
Gogendeau
Delphine
D
Katinka
Michael
M
Keller
Anne-Marie
AM
Kissmehl
Roland
R
Klotz
Catherine
C
Koll
France
F
Le Mouël
Anne
A
Lepère
Gersende
G
Malinsky
Sophie
S
Nowacki
Mariusz
M
Nowak
Jacek K
JK
Plattner
Helmut
H
Poulain
Julie
J
Ruiz
Françoise
F
Serrano
Vincent
V
Zagulski
Marek
M
Dessen
Philippe
P
Bétermier
Mireille
M
Weissenbach
Jean
J
Scarpelli
Claude
C
Schächter
Vincent
V
Sperling
Linda
L
Meyer
Eric
E
Cohen
Jean
J
Wincker
Patrick
P
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