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Synteny analysis provides a route to design genus-specific PCR primers for rapid identification of all Saccharomyces species.
- Source :
-
FEMS yeast research [FEMS Yeast Res] 2014 May; Vol. 14 (3), pp. 517-25. Date of Electronic Publication: 2013 Dec 04. - Publication Year :
- 2014
-
Abstract
- The genus Saccharomyces comprises seven single-genome species (S. arboricola, S. cerevisiae, S. eubayanus, S. kudriavzevii, S. mikatae, S. paradoxus and S. uvarum) and two hybrid species - S. pastorianus (S. cerevisiae plus S. eubayanus) and S. bayanus (mostly S. uvarum plus S. eubayanus). Species-specific primers have already been developed for the identification of each of the single-genome species, and these primers can usually detect both genomes in hybrids. It would be advantageous if a single reaction could detect any member of the clade. We have investigated three potentially generic approaches to design genus-specific primers. Two methods that both use sequence alignment differences for primer design were only partly successful. A third method used synteny data to identify 136 target genes that are potentially present only in all species of the Saccharomyces clade. HSP30 (YCR021C) was fully successful; different primer pairs were developed with high G+C content for use at 63 °C. In < 3 h, using a robust colony-PCR followed by gel electrophoresis, the method can reliably detect any member of the genus. This novel approach still uses conventional sequence alignment mismatches but relies principally on the presence of the target gene only within the genus Saccharomyces.<br /> (© 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)
- Subjects :
- Base Composition
DNA, Fungal chemistry
Electrophoresis
Fungal Proteins genetics
HSP30 Heat-Shock Proteins genetics
Molecular Sequence Data
Sequence Analysis, DNA
Temperature
Time Factors
DNA Primers genetics
DNA, Fungal genetics
Mycology methods
Polymerase Chain Reaction methods
Saccharomyces classification
Saccharomyces genetics
Synteny
Subjects
Details
- Language :
- English
- ISSN :
- 1567-1364
- Volume :
- 14
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- FEMS yeast research
- Publication Type :
- Academic Journal
- Accession number :
- 24215185
- Full Text :
- https://doi.org/10.1111/1567-1364.12124