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Originally published as Genetics Published Articles Ahead of Print on December 1, 2005.
Genetics, Vol. 172, 863-872, February 2006, Copyright © 2006
doi:10.1534/genetics.105.048900
After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes
Paul F. Cliften*,1,
Robert S. Fulton
,
Richard K. Wilson*, and
Mark Johnston*,2
* Department of Genetics and Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63110
2 Corresponding author: Department of Genetics, Campus Box 8232, Washington University Medical School, 660 S. Euclid Ave., St. Louis, MO 63110.
E-mail: mj{at}genetics.wustl.edu
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 (
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 9. 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.
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