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doi:10.1534/genetics.105.048900
A more recent version of this article appeared on February 1, 2006.
REGULAR RESEARCH PAPERS |
After the duplication: gene loss and adaptation in Saccharomyces genomes
Paul Cliften 1, Robert Fulton 2, Rick Wilson 2 and Mark Johnston 3*
1 Utah State University
2 Washington University Genome Sequencing Center
3 Washington University
* To whom correspondence should be addressed. E-mail: mj{at}genetics.wustl.edu.
Submitted on July 29, 2005
Revised on September 10, 2005
Accepted on 8 November 2005
ABSTRACT The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication event. To learn more about the evolutionary effects of the duplication event, we compared the S. cerevisiae genome to other Saccharomyces genomes. We demonstrate that the whole genome duplication occurred before S. castellii diverged from S. cerevisiae. In addition to more accurately dating the duplication event, this finding allowed us to study the effects of the duplication on two separate lineages. Analyses of the duplication regions of the genomes indicate that most of the duplicated genes (approximately 85%) were lost before the speciation. Only a small amount of paralogous gene loss (4-6%) occurred after speciation. On the other hand, S. castellii appears to have lost several hundred genes that were not retained as duplicated paralogs. These losses could be related to genomic rearrangements that reduced the number of chromosomes from 16 to nine. In addition to S. castellii, other Saccharomyces sensu lato species likely diverged from S. cerevisiae after the duplication. A thorough analysis of these species will likely reveal other important outcomes of the whole genome duplication.
Key Words: Saccharomyces phylogeny, comparative sequence analysis, genomic duplication, yeast
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