Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.
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.
Department of Biology, Indiana University.
Casey L
CL
McGrath
Department of Biology, Indiana University.
Jean-Francois
JF
Gout
Department of Biology, Indiana University National Center for Genome Analysis Support at Indiana University, Bloomington, Indiana 47405.
Thomas G
TG
Doak
Department of Human Education Faculty of Human Studies Ishinomaki Senshu University Ishinomaki 986-8580, Japan.
Akira
A
Yanagi
Department of Biology, Indiana University milynch@indiana.edu.
Michael
M
Lynch
D001482:Base Composition / Q000235:genetics; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D020440:Gene Duplication; D018503:Genome, Protozoan; D008957:Models, Genetic; D048488:Paramecium caudatum / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
Paramecium; genome evolution; polyploidization; speciation; whole-genome duplication