Yeast genome duplication was followed by asynchronous differentiation of duplicated genes

Abstract

Gene redundancy has been observed in yeast, plant and human genomes, and is thought to be a consequence of whole-genome duplications. Baker's yeast, Saccharomyces cerevisiae, contains several hundred duplicated genes. Duplication(s) could have occurred before or after a given speciation. To understand the evolution of the yeast genome, we analysed orthologues of some of these genes in several related yeast species. On the basis of the inferred phylogeny of each set of genes, we were able to deduce whether the gene duplicated and/or specialized before or after the divergence of two yeast lineages. Here we show that the gene duplications might have occurred as a single event, and that it probably took place before the Saccharomyces and Kluyveromyces lineages diverged from each other. Further evolution of each duplicated gene pair-such as specialization or differentiation of the two copies, or deletion of a single copy--has taken place independently throughout the evolution of these species.

Genome sequencing and analysis of Aspergillus oryzae

“…The speciation of Aspergillus was estimated to have taken place approximately 20 million years ago 15 and was later than the whole-genome duplication event in yeast, which was estimated to have taken place 150 million years ago 16 . We were unable to observe any extended stretch of region within the A. oryzae genome that showed a certain degree of similarity to another stretch of region despite the fact that we observed synteny among the three aspergilli ( Fig.…”

The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication

“…Gene duplication is thought to be a key mechanism by which networks evolve and new components are added (1)(2)(3)(4)(5)(6)43). These duplication events can act on a single gene, a chromosomal segment, or even a whole genome (1,(7)(8)(9)(10)(11). After duplication, the duplicate genes may assume one of several fates, including differentiation of sequence and function, or loss of one of the duplicates (12)(13)(14)(15)(16)(17)44).…”

“…After duplication, the duplicate genes may assume one of several fates, including differentiation of sequence and function, or loss of one of the duplicates (12)(13)(14)(15)(16)(17)44). These outcomes are thought to be affected by genetic factors including redundancy, modularization, and expression dosage (9,12,15,(18)(19)(20)(21)(22)45).…”

“…Our method decomposes a protein interaction network into a vector of network motifs and tracks the evolution of this vector over time. We apply our methodology to the protein interaction network of Saccharomyces cerevisiae (23-29), which has undergone a whole-genome duplication (WGD) event, resulting in hundreds of coordinately duplicated gene pairs (ohnologs) (8,9,11). …”

Elaboration, Diversification and Regulation of the Sir1 Family of Silencing Proteins in Saccharomyces

“…The genome duplication in the Saccharomyces lineage occurred once, and duplicated gene blocks were lost both before and after speciation events (Langkjaer et al 2003). If the last common ancestor of the Saccharomyces clade ( Figure 1A) had four Sir1 paralogs, then there must have been multiple loss events leading to S. cerevisiae and its closest neighbors.…”