The utility of iPBS retrotransposons markers to analyze genetic variation in yeast

Aydin, Furkan; Özer, Göksel; Alkan, Mehtap; Çakır, İbrahim

doi:10.1016/j.ijfoodmicro.2020.108647

Cited by 28 publications

(17 citation statements)

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“…Even in some cases, identification using molecular methods in which Internally Transcript Sequence (ITS) region is amplified by PCR makes some challenges to differentiate between species. Partial amplification of large subunit is often of choice (Aydin et al, 2020). Nnon-molecular techniques may not give the best results owing to the inherent phenotypic and genetic heterogeneity in populations, or the limited ability of phenotypic tests used to identify species.…”

Section: Results and Discussion Identification Of The Strains And Phylogenetic Analysesmentioning

confidence: 99%

“…There has been a growing interest in studying yeast isolated from traditional cheeses in recent years, which mainly focus on genetic characterization, determining their roles in ripening and evaluating their technological and probiotic characteristics more in particular (Aydin et al, 2020;Binetti et al, 2013). Four significant yeast species, which are Yarrowia lipolytica, Kluyveromyces marxianus, K. lactis, and Debaryomyces hansenii, were reported to be the most isolated species from artisanal cheeses and their brine solutions and are described in more detail (Atanassova et al, 2016;Banjara et al, 2015;Ceugniez et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Fermente Salamura Otlardan İzole Edi̇len Mayalarin Enzi̇mati̇k Karakteri̇zasyonu

Güneş

Aydin

Çakır

2021

Gıda

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This study aims to identify yeasts from spontaneously fermented herbs used for Van herby cheese and to evaluate their enzymatic activities. Sequencing of partial 26S rRNA gene revealed the species of Pichia membranifaciens (n = 8), Kazachstania servazzii (n = 6), Debaryomyces hansenii (n = 2), Kluyveromyces marxianus (n = 2), and Pichia fermentans (n = 2). Enzyme profiles were determined using API-ZYM strips. The isolates had diverse enzyme activities, including alkaline and acid phosphatase, esterase, esterase lipase, aminopeptidases, and proteases mostly at different levels, which may have crucial roles during ripening of the cheese. K. marxianus M8.1, D. hansenii M6.1, and M6.3, P. membraniciens M13.1, M13.2, and M14.1 had superior and diverse enzymatic characteristics. Such enzymatic activities could be of great technological importance for the determination of adjunct culture along with starter lactic acid bacteria for the production of Van herby cheese.

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Section: Results and Discussion Identification Of The Strains And Phylogenetic Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fermente Salamura Otlardan İzole Edi̇len Mayalarin Enzi̇mati̇k Karakteri̇zasyonu

Güneş

Aydin

Çakır

2021

Gıda

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“…Phylogenetic and molecular evolutionary analyses of sixty-two isolates from this study and the corresponding Enterococcus isolates in the GenBank nucleotide database (E. faecalis: NR114782, NR115765, NR040789; E. faecium: NR042054, NR114742, NR113904; E. durans: NR113257, NR036922) were aligned with ClustalW (Thompson et al, 1994). Phylogenetic trees were constructed using the Maximum-Likelihood method with bootstrap analyses in Mega X software (Kumar et al, 2018) as previously described by Aydin et al (2020) in detail.…”

Section: Molecular Identificationmentioning

confidence: 99%

Aksaray İli̇nde Satişa Sunulan Tulum Peyni̇rleri̇nden İzole Edi̇len Enterokoklarin Anti̇bi̇yoti̇k Di̇rençli̇li̇kleri̇ İle Hemoli̇ti̇k Akti̇vi̇teleri̇ni̇n Beli̇rlenmesi̇

Ayhan

Kahve

Aydin

et al. 2020

Gıda

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This study aimed to evaluate the hemolytic activity and antibiotic susceptibility of enterococci isolated from Tulum cheese samples sold in Aksaray province. The isolates were identified as E. faecium (n = 30), E. faecalis (n = 25), and E. durans (n = 7) as a result of 16S rRNA gene sequencing. Three strains (E. faecalis ATC12, E. faecium ATC49, and E. faecium ATC54) exhibited ß-hemolytic activity, whereas others were non-hemolytic. Enterococci were found to have an intermediary or high resistance to nalidixic acid (%100), oxacillin (92%), and streptomycin (72.6%), respectively. E. faecalis strains had more resistant phenotypes to various clinically significant antibiotics than E. faecium and E. durans. Multi-drug resistance was found in 41.93% of the isolates. According to the results, Tulum cheese produced in Aksaray could be a potential vehicle for the transmission of antibiotic resistance via the food chain.

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“…Kalendar et al (2010) introduced a universal retrotransposon-based DNA marker technique, inter-Primer Binding Site (iPBS) retrotransposons, without requiring prior sequence information. Aydin et al (2020) previously reported the utility of iPBS polymorphism in the yeast genome. The genetic variation in S. cerevisiae individuals was notably high, making this PCRbased marker method an excellent candidate to evaluate genetic differentiation and the population structure of S. cerevisiae.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of Saccharomyces cerevisiae isolated from Turkish sourdough by iPBS-retrotransposons markers

et al. 2022

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Molecular DNA markers are valuable tools for analyzing genetic variation among yeast from different populations to reveal the genetically different autochthonous strains. In this study, we employed inter-primer binding site (iPBS) retrotransposon polymorphism to assess the genetic variation and population structure of 96 Saccharomyces cerevisiae isolates from four different regions in Turkey. The nine selected iPBS primers amplified 102 reproducible and scorable bands, of which 95.10% were polymorphic with an average of 10.78 polymorphic fragments per primer. The average polymorphism information content and the resolving power were 0.26-3.58, respectively. Analysis of molecular variance (AMOVA) revealed significant (P < 0.001) genetic differences within populations (88%) and between populations (12%). The unweighted pair group mean with arithmetic (UPGMA) dendrogram grouped 96 S. cerevisiae strains into two main clusters, where the highest probability of the data elucidating the population structure was obtained at ΔK = 2. There was not an obvious genetic discrimination of the populations according to geographical regions on UPGMA, supported by principal coordinate analysis. However, the individuals of the closer provinces in each population were more likely to group together or closely. The results indicate that iPBS polymorphism is a useful tool to reveal the genetically diverse autochthonous S. cerevisiae strains that may be important for the production of sourdough or baked goods.

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The utility of iPBS retrotransposons markers to analyze genetic variation in yeast

Cited by 28 publications

References 50 publications

Fermente Salamura Otlardan İzole Edi̇len Mayalarin Enzi̇mati̇k Karakteri̇zasyonu

Fermente Salamura Otlardan İzole Edi̇len Mayalarin Enzi̇mati̇k Karakteri̇zasyonu

Aksaray İli̇nde Satişa Sunulan Tulum Peyni̇rleri̇nden İzole Edi̇len Enterokoklarin Anti̇bi̇yoti̇k Di̇rençli̇li̇kleri̇ İle Hemoli̇ti̇k Akti̇vi̇teleri̇ni̇n Beli̇rlenmesi̇

Genetic diversity and population structure of Saccharomyces cerevisiae isolated from Turkish sourdough by iPBS-retrotransposons markers

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