Skip Navigation



MBE Advance Access published online on March 9, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj121
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/6/1136    most recent
msj121v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Byrnes, J. K.
Right arrow Articles by Li, W.-H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Byrnes, J. K.
Right arrow Articles by Li, W.-H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted March 1, 2006

Research Article

Reorganization of Adjacent Gene Relationships in Yeast Genomes by Whole Genome Duplication and Gene Deletion

Jake K. Byrnes 1 *, Geoffrey P. Morris 1 *, and Wen-Hsiung Li 1 *

1 Department of Ecology and Evolution, University of Chicago

* To whom correspondence should be addressed.
Wen-Hsiung Li, E-mail: whli{at}uchicago.edu


  Abstract

In Saccharomyces, an ancient whole genome duplication (WGD) and widespread duplicate gene deletion resulted in extensive reorganization of adjacent gene relationships. We have studied the evolution of adjacent gene pairs' identity, orientation, and spacing following WGD and deletion (WGD-D) using comparative genomic analyses and simulations. Surveying adjacent gene organization across the Saccharomyces species complex, we find a genome-wide bias towards divergently and convergently transcribed gene pairs in all species, but a reduction in this bias in the species that underwent WGD-D. Among neutral models of WGD-D, only single-gene deletion can produce the appropriate reduction in orientation bias and recapitulate the pattern of short, highly-dispersed deletions we observe in S. cerevisiae. To characterize the dynamics of WGD-D, we trace the conservation and creation of adjacent gene pairs along the S. cerevisiae lineage. We find that newly created adjacencies have a tandem orientation bias, while adjacencies conserved from prior to WGD-D have the same divergent-convergent bias as found in the species that diverged before WGD. We also find that adjacent gene pairs produced by WGD-D gained greater intergenic spacing, but that this is reduced in the older adjacencies. Given this, and the preponderance of short deleted blocks, we argue that the deletion phase of WGD-D occurred primarily by small inactivating mutations followed by numerous small deletions. Newly created adjacent gene pairs also have an initial increase in mean log2 expression ratios and maximal expression levels, suggesting that increased intergenic spacing caused a genome-wide reduction in transcriptional interference.

Keywords: Whole genome duplication; gene deletion; Saccharomyces ; adjacent gene orientation; intergenic spacing; gene expression.

*These authors contributed equally.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
B. Dunn and G. Sherlock
Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus
Genome Res., October 1, 2008; 18(10): 1610 - 1623.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B.-Y. Liao and J. Zhang
Coexpression of Linked Genes in Mammalian Genomes Is Generally Disadvantageous
Mol. Biol. Evol., August 1, 2008; 25(8): 1555 - 1565.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. J. A. van Hoek and P. Hogeweg
The Role of Mutational Dynamics in Genome Shrinkage
Mol. Biol. Evol., November 1, 2007; 24(11): 2485 - 2494.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
M. Woolfit, E. Rozpedowska, J. Piskur, and K. H. Wolfe
Genome Survey Sequencing of the Wine Spoilage Yeast Dekkera (Brettanomyces) bruxellensis
Eukaryot. Cell, April 1, 2007; 6(4): 721 - 733.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. P. Byrne and K. H. Wolfe
Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication
Genetics, March 1, 2007; 175(3): 1341 - 1350.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. G. Giacomelli, A. S. Hancock, and J. Masel
The Conversion of 3' UTRs into Coding Regions
Mol. Biol. Evol., February 1, 2007; 24(2): 457 - 464.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Barrett, D. B. Troup, S. E. Wilhite, P. Ledoux, D. Rudnev, C. Evangelista, I. F. Kim, A. Soboleva, M. Tomashevsky, and R. Edgar
NCBI GEO: mining tens of millions of expression profiles--database and tools update
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D760 - D765.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.