@misc{oai:ir.soken.ac.jp:00002714,
 author = {杉野, 隆一 and スギノ, リュウイチ and SUGINO, Ryuichi},
 month = {2016-02-17, 2016-02-17},
 note = {  My research interest is to understand the mechanisms of evolution on a genomicscale. Recent advances of genome sequencing technology and genomewideexperimental technology provide an excellent opportunity of studies of genomeevolution. In my PhD work, using the bakers’ yeast Saccharomyces cerevisiae asa model, I studied genome evolution after a whole-genome duplication (WGD)event. All genes were doubled at the WGD event, but only   10 % of them remainas duplicates (called ohnologs) at present and other genes have lost one ofthe duplicated pairs. In addition, massive genome rearrangement have occurred inthis gene deletion process.
  This thesis was constructed by three parts. In the first part, I studied the evolutionof ohnologs. Interlocus gene conversion is a unique recombinational mechanismto duplicated genes. Because it retards the nucleotide divergence of duplicates,the standard molecular clock model can not be directly applied to infer thehistory of duplicates. In this chapter, a maximum likelihood method to estimatethe time of the WGD was developed incorporating the effect of gene conversion.It was estimated that the WGD is almost as old as the speciation event with pre-WGD species. It is suggested that the WGD might have caused the speciation.
  In the next part, I examined the role of natural selection to the duration ofconcerted evolution. It was found that duplicated with higher expression (especiallyribosome and histone genes) prefers long-term concerted evolution, indicatinggene conversion may be favored for such high-demand genes. By genomewidedata analysis with various kinds of experimental data, I found this hypothesisis a likely explanation of the observation.
  In the third part, I studied the evolution of gene order in the genome rearrangementprocess after the WGD. In the analysis I focused on adjacent genepairs. Comparative genome analysis indicated that newly generated adjacent genepairs in divergent orientation are relatively rare and they have on average longintergenic distances and low coexpression. I considered that the locations of nucleosomefree regions (NFRs) would explain this. It is known that transcriptionstart in both directions when Pol II binds to a NFR. It is predicted that such coexpressionwould be deleterious for a random pair of genes that happened to beadjacent to each other. If so, selection should have worked against deletion betweennewly created divergent gene pairs, thereby keeping them physically awayso that their coexpression might be avoided. I verified this hypothesis by comparativegenomic analysis of the locations of NFRs and evolutionary simulations.
  Through these works, I conclude that the genome of S. cerevisiae undergo varioustypes of genome-wide natural selection through the process after the WGD.This study also shows that the post-genomic biological data are useful to determinethe target of natural selection., application/pdf, 総研大甲第1465号},
 title = {Genome evolution after WGD in the baker's yeast.},
 year = {}
}