Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence

Casey L. McGrath, Jean Francois Gout, Thomas G. Doak, Akira Yanagi, Michael Lynch

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event.

Original languageEnglish (US)
Pages (from-to)1417-1428
Number of pages12
JournalGenetics
Volume197
Issue number4
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

Fingerprint

Paramecium caudatum
Genome
Paramecium tetraurelia
Paramecium
Reproductive Isolation
Gene Duplication
Gene Dosage
Base Composition
Eukaryota

Keywords

  • Genome evolution
  • Paramecium
  • Polyploidization
  • Speciation
  • Whole-genome duplication

ASJC Scopus subject areas

  • Genetics

Cite this

Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. / McGrath, Casey L.; Gout, Jean Francois; Doak, Thomas G.; Yanagi, Akira; Lynch, Michael.

In: Genetics, Vol. 197, No. 4, 01.01.2014, p. 1417-1428.

Research output: Contribution to journalArticle

McGrath, Casey L. ; Gout, Jean Francois ; Doak, Thomas G. ; Yanagi, Akira ; Lynch, Michael. / Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. In: Genetics. 2014 ; Vol. 197, No. 4. pp. 1417-1428.
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