Limits...
New primers for promising single-copy genes in fungal phylogenetics and systematics.

Schmitt I, Crespo A, Divakar PK, Fankhauser JD, Herman-Sackett E, Kalb K, Nelsen MP, Nelson NA, Rivas-Plata E, Shimp AD, Widhelm T, Lumbsch HT - Persoonia (2009)

Bottom Line: Developing powerful phylogenetic markers is a key concern in fungal phylogenetics.Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class.We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology and Bell Museum of Natural History, University of Minnesota, 1445 Gortner Ave, St. Paul, MN 55108, USA;

ABSTRACT
Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota.

No MeSH data available.


Related in: MedlinePlus

Comparison of the new primers to homologous sequences in Saccharomycotina (Ashbya, Kluyveromyces, Saccharomyces, Yarrowia), Taphrinomycotina (Schizosaccharomyces) and Basidiomycota (Coprinopsis, Cryptococcus, Ustilago). 100 % matches between primer sequence and gene sequences studied are indicated by grey shading. High sequence similarities indicate that the new primers are likely to fit in members of the analysed groups. Some primer sequences may require slight modifications.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2802727&req=5

Figure 3: Comparison of the new primers to homologous sequences in Saccharomycotina (Ashbya, Kluyveromyces, Saccharomyces, Yarrowia), Taphrinomycotina (Schizosaccharomyces) and Basidiomycota (Coprinopsis, Cryptococcus, Ustilago). 100 % matches between primer sequence and gene sequences studied are indicated by grey shading. High sequence similarities indicate that the new primers are likely to fit in members of the analysed groups. Some primer sequences may require slight modifications.

Mentions: We aligned selected members of Saccharomycotina, Taphrinomycotina and Basidiomycota (Table 4) with our datasets and compared the new primer sequences to the corresponding positions in these taxa. The low number of mismatches suggests that the new primers will need no adjustments or only minor modifications to also fit these phylogenetic groups (Fig. 3).


New primers for promising single-copy genes in fungal phylogenetics and systematics.

Schmitt I, Crespo A, Divakar PK, Fankhauser JD, Herman-Sackett E, Kalb K, Nelsen MP, Nelson NA, Rivas-Plata E, Shimp AD, Widhelm T, Lumbsch HT - Persoonia (2009)

Comparison of the new primers to homologous sequences in Saccharomycotina (Ashbya, Kluyveromyces, Saccharomyces, Yarrowia), Taphrinomycotina (Schizosaccharomyces) and Basidiomycota (Coprinopsis, Cryptococcus, Ustilago). 100 % matches between primer sequence and gene sequences studied are indicated by grey shading. High sequence similarities indicate that the new primers are likely to fit in members of the analysed groups. Some primer sequences may require slight modifications.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2802727&req=5

Figure 3: Comparison of the new primers to homologous sequences in Saccharomycotina (Ashbya, Kluyveromyces, Saccharomyces, Yarrowia), Taphrinomycotina (Schizosaccharomyces) and Basidiomycota (Coprinopsis, Cryptococcus, Ustilago). 100 % matches between primer sequence and gene sequences studied are indicated by grey shading. High sequence similarities indicate that the new primers are likely to fit in members of the analysed groups. Some primer sequences may require slight modifications.
Mentions: We aligned selected members of Saccharomycotina, Taphrinomycotina and Basidiomycota (Table 4) with our datasets and compared the new primer sequences to the corresponding positions in these taxa. The low number of mismatches suggests that the new primers will need no adjustments or only minor modifications to also fit these phylogenetic groups (Fig. 3).

Bottom Line: Developing powerful phylogenetic markers is a key concern in fungal phylogenetics.Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class.We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology and Bell Museum of Natural History, University of Minnesota, 1445 Gortner Ave, St. Paul, MN 55108, USA;

ABSTRACT
Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota.

No MeSH data available.


Related in: MedlinePlus