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פותח על ידי קלירמאש פתרונות בע"מ -
Application of SNPs for assessing biodiversity and phylogeny among yeast strains
Year:
2005
Source of publication :
Heredity
Authors :
בן-ארי, גיורא
;
.
לביא, אורי
;
.
שרמן, עמיר
;
.
Volume :
95
Co-Authors:
Ben-Ari, G., Robert H. Smith Institute of Plant Sciences and Genetics, Hebrew University of Jerusalem, Rehovot 76100, Israel, Samuel Lunenfeld Research Institute, System Biology, Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ont. M5G 1X5, Canada
Zenvirth, D., Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
Sherman, A., Institute of Horticulture, ARO-Volcani Center, PO Box 6, Bet-Dagan 50250, Israel
Simchen, G., Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
Lavi, U., Institute of Horticulture, ARO-Volcani Center, PO Box 6, Bet-Dagan 50250, Israel
Hillel, J., Robert H. Smith Institute of Plant Sciences and Genetics, Hebrew University of Jerusalem, Rehovot 76100, Israel
Facilitators :
From page:
493
To page:
501
(
Total pages:
9
)
Abstract:
We examined the efficacy of single-nucleotide polymorphism (SNP) markers for the assessment of the phylogeny and biodiversity of Saccharomyces strains. Each of 32 Saccharomyces cerevisiae strains was genotyped at 30 SNP loci discovered by sequence alignment of the S. cerevisiae laboratory strain SK1 to the database sequence of strain S288c. In total, 10 SNPs were selected from each of the following three categories: promoter regions, nonsynonymous and synonymous sites (in open reading frames). The strains in this study included 11 haploid laboratory strains used for genetic studies and 21 diploids. Three non-cerevisiae species of Saccharomyces (sensu stricto) were used as an out-group. A Bayesian clustering-algorithm, Structure, effectively identified four different strain groups: laboratory, wine, other diploids and the non-cerevisiae species. Analysing haploid and diploid strains together caused problems for phylogeny reconstruction, but not for the clustering produced by Structure. The ascertainment bias introduced by the SNP discovery method caused difficulty in the phylogenetic analysis; alternative options are proposed. A smaller data set, comprising only the nine most polymorphic loci, was sufficient to obtain most features of the results. © 2005 Nature Publishing Group All rights reserved.
Note:
Related Files :
biodiversity
Cluster analysis
Genetic distance
Genetics
Yeast
עוד תגיות
תוכן קשור
More details
DOI :
10.1038/sj.hdy.6800759
Article number:
0
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
22667
Last updated date:
02/03/2022 17:27
Creation date:
16/04/2018 23:53
Scientific Publication
Application of SNPs for assessing biodiversity and phylogeny among yeast strains
95
Ben-Ari, G., Robert H. Smith Institute of Plant Sciences and Genetics, Hebrew University of Jerusalem, Rehovot 76100, Israel, Samuel Lunenfeld Research Institute, System Biology, Institute at Mount Sinai Hospital, 600 University Avenue, Toronto, Ont. M5G 1X5, Canada
Zenvirth, D., Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
Sherman, A., Institute of Horticulture, ARO-Volcani Center, PO Box 6, Bet-Dagan 50250, Israel
Simchen, G., Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
Lavi, U., Institute of Horticulture, ARO-Volcani Center, PO Box 6, Bet-Dagan 50250, Israel
Hillel, J., Robert H. Smith Institute of Plant Sciences and Genetics, Hebrew University of Jerusalem, Rehovot 76100, Israel
Application of SNPs for assessing biodiversity and phylogeny among yeast strains
We examined the efficacy of single-nucleotide polymorphism (SNP) markers for the assessment of the phylogeny and biodiversity of Saccharomyces strains. Each of 32 Saccharomyces cerevisiae strains was genotyped at 30 SNP loci discovered by sequence alignment of the S. cerevisiae laboratory strain SK1 to the database sequence of strain S288c. In total, 10 SNPs were selected from each of the following three categories: promoter regions, nonsynonymous and synonymous sites (in open reading frames). The strains in this study included 11 haploid laboratory strains used for genetic studies and 21 diploids. Three non-cerevisiae species of Saccharomyces (sensu stricto) were used as an out-group. A Bayesian clustering-algorithm, Structure, effectively identified four different strain groups: laboratory, wine, other diploids and the non-cerevisiae species. Analysing haploid and diploid strains together caused problems for phylogeny reconstruction, but not for the clustering produced by Structure. The ascertainment bias introduced by the SNP discovery method caused difficulty in the phylogenetic analysis; alternative options are proposed. A smaller data set, comprising only the nine most polymorphic loci, was sufficient to obtain most features of the results. © 2005 Nature Publishing Group All rights reserved.
Scientific Publication
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