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Retrotransposon microsatellite amplified polymorphism strain fingerprinting markers applicable to various mushroom species.

Le QV, Won HK, Lee TS, Lee CY, Lee HS, Ro HS - Mycobiology (2008)

Bottom Line: To utilize marY1 as a molecular marker for the DNA fingerprinting of mushrooms, oligonucleotides marY1-LTR-L and marY1-LTR-R were designed on the basis of highly conserved regions from the multiple sequence alignment of 30 marY1 sequences retrieved from a nucleotide sequence database.In accordance with Retrotransposon Microsatellite Amplified Polymorphism (REMAP) fingerprinting methodology, the two oligonucleotides were utilized together with the short sequence repeat primers UBC807 and UBC818 for polymerase chain reaction using templates from different mushroom genomic DNAs.Among the tested oligonucleotides, the marY1-LTR-L and UBC807 primer set yielded the greatest amount of abundance and variation in terms of DNA band numbers and patterns.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Research Institute of Life Sciences, Gyeongsang National University, Chinju 660-701, Korea.

ABSTRACT
The retrotransposon marY1 is a gypsy family retroelement, which is detected ubiquitously within the fungal taxonomic groups in which mushrooms are included. To utilize marY1 as a molecular marker for the DNA fingerprinting of mushrooms, oligonucleotides marY1-LTR-L and marY1-LTR-R were designed on the basis of highly conserved regions from the multiple sequence alignment of 30 marY1 sequences retrieved from a nucleotide sequence database. In accordance with Retrotransposon Microsatellite Amplified Polymorphism (REMAP) fingerprinting methodology, the two oligonucleotides were utilized together with the short sequence repeat primers UBC807 and UBC818 for polymerase chain reaction using templates from different mushroom genomic DNAs. Among the tested oligonucleotides, the marY1-LTR-L and UBC807 primer set yielded the greatest amount of abundance and variation in terms of DNA band numbers and patterns. This method was successfully applied to 10 mushroom species, and the primer set successfully discriminated between different commercial mushroom cultivars of the same strains of 14 Pleurotus ostreatus and 16 P. eryngii. REMAP reproducibility was superior to other popular DNA fingerprinting methodologies including the random amplified polymorphic DNA method.

No MeSH data available.


REMAP analyses on the mushroom strains within the same species. Band patterns and dendrograms of 14 P. ostreatus strains (A and B, respectively) and 16 P. eryngii strains (C and D, respectively) are displayed. The 14 P. ostreatus strains identified by lane are: 1, IUM1051; 2, IUM1313; 3, IUM1367; 4, IUM1490; 5, IUM1556; 6, IUM1491; 7, IUM557; 8, IUM1677; 9, IUM165; 10, IUM778; 11, IUM1520; 12, IUM1373; 13, IUM1341; 14, IUM1346. Similarly, the 16 P. eryngii strains are: 1, IUM2501; 2, IUM2502; 3, IUM2503; 4, IUM2510; 5, IUM1511; 6, IUM2512; 7, IUM2513; 8, IUM2514; 9, IUM2515; 10, IUM2518; 11, IUM2519; 12, IUM2520; 13, IUM2521; 14, IUM2523; 15, IUM2524; 16, IUM2322. The patterns of DNA bands were analyzed and dendograms were created with Bio-1D++.
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Figure 4: REMAP analyses on the mushroom strains within the same species. Band patterns and dendrograms of 14 P. ostreatus strains (A and B, respectively) and 16 P. eryngii strains (C and D, respectively) are displayed. The 14 P. ostreatus strains identified by lane are: 1, IUM1051; 2, IUM1313; 3, IUM1367; 4, IUM1490; 5, IUM1556; 6, IUM1491; 7, IUM557; 8, IUM1677; 9, IUM165; 10, IUM778; 11, IUM1520; 12, IUM1373; 13, IUM1341; 14, IUM1346. Similarly, the 16 P. eryngii strains are: 1, IUM2501; 2, IUM2502; 3, IUM2503; 4, IUM2510; 5, IUM1511; 6, IUM2512; 7, IUM2513; 8, IUM2514; 9, IUM2515; 10, IUM2518; 11, IUM2519; 12, IUM2520; 13, IUM2521; 14, IUM2523; 15, IUM2524; 16, IUM2322. The patterns of DNA bands were analyzed and dendograms were created with Bio-1D++.

Mentions: As shown in Fig. 3, the Com3 primer set verified their feasibility in generating gel patterns for the genotyping of mushroom strains. Fourteen cultivars of P. ostreatus (Fig. 4A) and 16 cultivars of P. eryngii (Fig. 4C) were selected and subjected to REMAP. Variations in the band patterns are more distinctively evident in adjacent dendrograms (Fig. 4B and 4D).


Retrotransposon microsatellite amplified polymorphism strain fingerprinting markers applicable to various mushroom species.

Le QV, Won HK, Lee TS, Lee CY, Lee HS, Ro HS - Mycobiology (2008)

REMAP analyses on the mushroom strains within the same species. Band patterns and dendrograms of 14 P. ostreatus strains (A and B, respectively) and 16 P. eryngii strains (C and D, respectively) are displayed. The 14 P. ostreatus strains identified by lane are: 1, IUM1051; 2, IUM1313; 3, IUM1367; 4, IUM1490; 5, IUM1556; 6, IUM1491; 7, IUM557; 8, IUM1677; 9, IUM165; 10, IUM778; 11, IUM1520; 12, IUM1373; 13, IUM1341; 14, IUM1346. Similarly, the 16 P. eryngii strains are: 1, IUM2501; 2, IUM2502; 3, IUM2503; 4, IUM2510; 5, IUM1511; 6, IUM2512; 7, IUM2513; 8, IUM2514; 9, IUM2515; 10, IUM2518; 11, IUM2519; 12, IUM2520; 13, IUM2521; 14, IUM2523; 15, IUM2524; 16, IUM2322. The patterns of DNA bands were analyzed and dendograms were created with Bio-1D++.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3755187&req=5

Figure 4: REMAP analyses on the mushroom strains within the same species. Band patterns and dendrograms of 14 P. ostreatus strains (A and B, respectively) and 16 P. eryngii strains (C and D, respectively) are displayed. The 14 P. ostreatus strains identified by lane are: 1, IUM1051; 2, IUM1313; 3, IUM1367; 4, IUM1490; 5, IUM1556; 6, IUM1491; 7, IUM557; 8, IUM1677; 9, IUM165; 10, IUM778; 11, IUM1520; 12, IUM1373; 13, IUM1341; 14, IUM1346. Similarly, the 16 P. eryngii strains are: 1, IUM2501; 2, IUM2502; 3, IUM2503; 4, IUM2510; 5, IUM1511; 6, IUM2512; 7, IUM2513; 8, IUM2514; 9, IUM2515; 10, IUM2518; 11, IUM2519; 12, IUM2520; 13, IUM2521; 14, IUM2523; 15, IUM2524; 16, IUM2322. The patterns of DNA bands were analyzed and dendograms were created with Bio-1D++.
Mentions: As shown in Fig. 3, the Com3 primer set verified their feasibility in generating gel patterns for the genotyping of mushroom strains. Fourteen cultivars of P. ostreatus (Fig. 4A) and 16 cultivars of P. eryngii (Fig. 4C) were selected and subjected to REMAP. Variations in the band patterns are more distinctively evident in adjacent dendrograms (Fig. 4B and 4D).

Bottom Line: To utilize marY1 as a molecular marker for the DNA fingerprinting of mushrooms, oligonucleotides marY1-LTR-L and marY1-LTR-R were designed on the basis of highly conserved regions from the multiple sequence alignment of 30 marY1 sequences retrieved from a nucleotide sequence database.In accordance with Retrotransposon Microsatellite Amplified Polymorphism (REMAP) fingerprinting methodology, the two oligonucleotides were utilized together with the short sequence repeat primers UBC807 and UBC818 for polymerase chain reaction using templates from different mushroom genomic DNAs.Among the tested oligonucleotides, the marY1-LTR-L and UBC807 primer set yielded the greatest amount of abundance and variation in terms of DNA band numbers and patterns.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Research Institute of Life Sciences, Gyeongsang National University, Chinju 660-701, Korea.

ABSTRACT
The retrotransposon marY1 is a gypsy family retroelement, which is detected ubiquitously within the fungal taxonomic groups in which mushrooms are included. To utilize marY1 as a molecular marker for the DNA fingerprinting of mushrooms, oligonucleotides marY1-LTR-L and marY1-LTR-R were designed on the basis of highly conserved regions from the multiple sequence alignment of 30 marY1 sequences retrieved from a nucleotide sequence database. In accordance with Retrotransposon Microsatellite Amplified Polymorphism (REMAP) fingerprinting methodology, the two oligonucleotides were utilized together with the short sequence repeat primers UBC807 and UBC818 for polymerase chain reaction using templates from different mushroom genomic DNAs. Among the tested oligonucleotides, the marY1-LTR-L and UBC807 primer set yielded the greatest amount of abundance and variation in terms of DNA band numbers and patterns. This method was successfully applied to 10 mushroom species, and the primer set successfully discriminated between different commercial mushroom cultivars of the same strains of 14 Pleurotus ostreatus and 16 P. eryngii. REMAP reproducibility was superior to other popular DNA fingerprinting methodologies including the random amplified polymorphic DNA method.

No MeSH data available.