Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion

Molecular Biology and Evolution
Jake K ByrnesWen-Hsiung Li

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 whole-genome duplication 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 toward 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 Saccharomyces 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 i...Continue Reading

Citations

Jun 19, 2010·Nature Reviews. Genetics·Bernard Dujon
Nov 14, 2006·Molecular Biology and Evolution·Michael G GiacomelliJoanna Masel
Apr 29, 2008·Molecular Biology and Evolution·Ben-Yang Liao, Jianzhi Zhang
May 7, 2011·Molecular Biology and Evolution·Ryuichi P Sugino, Hideki Innan
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Jun 10, 2009·Journal of Bioinformatics and Computational Biology·Chunfang ZhengDavid Sankoff
Dec 22, 2011·BMC Bioinformatics·Baoyong WangDavid Sankoff
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Aug 20, 2009·Molecular Systems Biology·Antoine Buetti-DinhAttila Becskei
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Dec 19, 2015·BMC Bioinformatics·David SankoffCarlos Abad Najar
Jul 11, 2007·Yeast·Devin R ScannellKenneth H Wolfe

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