Global trends of whole genome duplications revealed by the genome sequence of the ciliate Paramecium tetraurelia
Jean-Marc Aury
,
Olivier Jaillon
,
* Laurent Duret
,
Benjamin Noel
,
Claire Jubin
,
Betina M. Porcel
,
Béatrice Ségurens
,
Vincent Daubin
,
Véronique Anthouard
,
Nathalie Aiach
,
Olivier Arnaiz
,
Alain Billaut
,
Janine Beisson
,
Isabelle Blanc
,
Khaled Bouhouche
(1)
,
Francisco Câmara
,
Sandra Duharcourt
(1)
,
Roderic Guigo
,
Delphine Gogendeau
,
Michael Katinka
,
Anne-Marie Keller
,
Roland Kissmehl
,
Catherine Klotz
,
France Koll
,
Anne Le Mouël
(1)
,
Gersende Lepère
(1)
,
Sophie Malinsky
(1)
,
Mariusz Nowacki
(1)
,
Jacek K. Nowak
,
Helmut Plattner
,
Julie Poulain
(2)
,
Françoise Ruiz
,
Vincent Serrano
(1)
,
Marek Zagulski
,
Philippe Dessen
,
Mireille Bétermier
(1)
,
Jean Weissenbach
(3)
,
Claude Scarpelli
,
Vincent Schächter
,
Linda Sperlin
,
Eric Meyer
(1)
,
Jean Cohen
,
Patrick Wincker
(4)
Jean-Marc Aury
- Function : Author
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- IdHAL : jean-marc-aury
- ORCID : 0000-0003-1718-3010
Olivier Jaillon
- Function : Author
- PersonId : 756900
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- IdRef : 119733374
* Laurent Duret
- Function : Author
- PersonId : 21674
- IdHAL : laurent-duret
- ORCID : 0000-0003-2836-3463
- IdRef : 086039202
Benjamin Noel
- Function : Author
Claire Jubin
- Function : Author
Betina M. Porcel
- Function : Author
Béatrice Ségurens
- Function : Author
Vincent Daubin
- Function : Author
- PersonId : 169665
- IdHAL : vincent-daubin
- ORCID : 0000-0001-8269-9430
- IdRef : 088715000
Véronique Anthouard
- Function : Author
Nathalie Aiach
- Function : Author
Olivier Arnaiz
- Function : Author
- PersonId : 756901
- ORCID : 0000-0002-9626-1015
- IdRef : 253728738
Alain Billaut
- Function : Author
Janine Beisson
- Function : Author
Isabelle Blanc
- Function : Author
- PersonId : 8381
- IdHAL : isabelle-blanc
- ORCID : 0000-0002-1115-0536
- IdRef : 171319354
Francisco Câmara
- Function : Author
Sandra Duharcourt
- Function : Author
- PersonId : 738361
- IdHAL : sandra-duharcourt
- ORCID : 0000-0002-8913-8799
- IdRef : 181215497
Roderic Guigo
- Function : Author
Delphine Gogendeau
- Function : Author
Michael Katinka
- Function : Author
Anne-Marie Keller
- Function : Author
Roland Kissmehl
- Function : Author
- PersonId : 834786
Catherine Klotz
- Function : Author
France Koll
- Function : Author
Sophie Malinsky
- Function : Author
- PersonId : 756902
- ORCID : 0000-0002-8268-0067
Jacek K. Nowak
- Function : Author
Helmut Plattner
- Function : Author
Julie Poulain
- Function : Author
- PersonId : 756903
- ORCID : 0000-0002-8744-3116
- IdRef : 061407232
Françoise Ruiz
- Function : Author
Marek Zagulski
- Function : Author
Philippe Dessen
- Function : Author
- PersonId : 756813
- ORCID : 0000-0002-4799-5071
Mireille Bétermier
- Function : Author
- PersonId : 737516
- IdHAL : mireille-betermier
- ORCID : 0000-0002-5407-6292
- IdRef : 15530576X
Claude Scarpelli
- Function : Author
Vincent Schächter
- Function : Author
Linda Sperlin
- Function : Author
Eric Meyer
- Function : Author
- PersonId : 750632
- IdHAL : eric-meyer
- ORCID : 0000-0002-3161-8597
- IdRef : 075084724
Jean Cohen
- Function : Author
- PersonId : 838156
Patrick Wincker
- Function : Author
- PersonId : 757160
- ORCID : 0000-0001-7562-3454
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.