A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis

Bruns, Thomas D.; Szaro, Timothy M.; Gardes, Monique; Cullings, Ken; Pan, Jiao; Taylor, D. Lee; Horton, Thomas R.; Kretzer, Annette M.; Garbelotto, Matteo; Li, Y.

doi:10.1046/j.1365-294x.1998.00337.x

Cited by 261 publications

(225 citation statements)

References 40 publications

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“…Parts of these regions could not be aligned unambiguously. Our findings are consistent with results obtained from basidiomycetes, often showing species-specific length mutations in mitochondrial rDNA (Bruns & Szaro 1992;Hibbett & Donoghue 1995;Bruns et al 1998;Gonzales & Labarere 1998). This variation together with nucleotide substitutions has been proved to be useful for phylogenetic studies.…”

Section: Resultssupporting

confidence: 92%

Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes

Zoller¹,

Scheidegger²,

Sperisen³

1999

The Lichenologist

375

292

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Four primers for the amplification of mitochondrial DNA of lichenforming ascomycetes are presented. The primers match the conserved regions U2, U4, and U6, respectively, of mitochondrial small subunit (SSU) ribosomal DNA (rDNA). Polymerase chain reaction using different combinations of the primers produced single amplification products from DNA of eight lichen-forming fungal species but did not amplify DNA of two axenic cultured algal species. The amplification product obtained from Lobaria pulmonaria was sequenced and the 894-bp sequence was compared with the mitochondrial SSU rDNA sequence of Podospora anserina. The two sequences revealed more than 76% identity in the conserved regions U3 to U5 demonstrating that we amplified mitochondrial DNA. The primers matching U2 and U6 yielded amplification products of 800-1000 bp depending on the species examined. The variation observed suggests that mitochondrial SSU rDNA may be useful for phylogenetic analyses of lichen-forming ascomycetes.

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Section: Resultssupporting

confidence: 92%

Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes

Zoller¹,

Scheidegger²,

Sperisen³

1999

The Lichenologist

375

292

View full text Add to dashboard Cite

show abstract

“…DNA was extracted from ectomycorrhizas in cetyl trimethylammonium bromide with chloroform and amplified in polymerase chain reactions (PCR) with fungal specific primers ITS1F and ITS4 (White et al 1990, Gardes and Bruns 1993, Bruns et al 1998 Altschul et al 1990). Identifications were based on strength of match, similarity over the entire fragment length, consistency of matches, the pattern of top matches to vouchered specimens, and dissimilarity to other genera.…”

Section: Molecular Methodsmentioning

confidence: 99%

Ectomycorrhizal communities of Quercus garryana are similar on serpentine and nonserpentine soils

et al. 2008

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Serpentine soils, rich in iron, magnesium, and heavy metals, select for unique plant communities and for endemic species. Because mycorrhizal fungi mediate the interaction between plants and soil, we hypothesized that distinct ectomycorrhizal fungi would colonize Quercus garryana roots on serpentine and nonserpentine soils. We sampled roots of Q. garryana on serpentine soils at two locations in the Klamath-Siskiyou Mountains of southwestern Oregon and identified ectomycorrhizas by morphological and molecular methods. The same six most abundant and most frequent mycorrhizal species, Cenococcum geophilum, Tuber candidum, Genea harknessii, Tomentella sp., Sebacina sp., and Inocybe sp., were found on serpentine and nonserpentine soils. Based on similarities calculated using the Sørensen index in Non-metric Multidimensional Scaling, mycorrhizal communities on serpentine and nonserpentine soils were not significantly different. This study showed that ectomycorrhizal species associated with Q. garryana exhibit edaphic tolerance and were neither reduced nor excluded by serpentinite or peridotite parent materials.

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“…On the other hand, this is the first time that the existence of group II introns with additional nucleotides at the 59 end is explicitly reported (the presence of a 59 terminal insert in the Agrocybe aegerita LSU2059 intron was apparent in the secondary structure model in Figure 3 of Gonzalez et al ½1999 but was not discussed in the text). 59-Terminal inserts can be surprisingly long: In Paxillus atrotomentosus isolate TDB-782 (Bruns et al 1998), an intron closely related to the LSU2059 intron of Suillus luteus has no fewer than 48 additional nucleotides inserted between the presumed 59 splice site and the UAGCGAC sequence motif that these two introns share on the 59 side of domain I (this sequence ½accession number AD001614 was not listed in Table 1 because it stops 73 nt within the intron). At the other end of the length spectrum, only 1 nt separates the inferred 59 splice site from the canonical GUGCG sequence motif in the three placozoan LSU2586 sequences.…”

Section: Discussionmentioning

confidence: 99%

Recurrent insertion of 5′-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs

Costa²,

Bassi³

et al. 2011

RNA

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A survey of sequence databases revealed 10 instances of subgroup IIB1 mitochondrial ribosomal introns with 1 to 33 additional nucleotides inserted between the 59 exon and the consensus sequence at the intron 59 end. These 10 introns depart further from the IIB1 consensus in their predicted domain VI structure: In contrast to its basal helix and distal GNRA terminal loop, the middle part of domain VI is highly variable and lacks the bulging A that serves as the branchpoint in lariat formation. In vitro experiments using two closely related IIB1 members inserted at the same ribosomal RNA site in the basidiomycete fungi Grifola frondosa and Pycnoporellus fulgens revealed that both ribozymes are capable of efficient self-splicing. However, whereas the Grifola intron was excised predominantly as a lariat, the Pycnoporellus intron, which possesses six additional nucleotides at the 59 end, yielded only linear products, consistent with its predicted domain VI structure. Strikingly, all of the introns with 59 terminal insertions lack the EBS2 exon-binding site. Moreover, several of them are part of the small subset of group II introns that encode potentially functional homing endonucleases of the LAGLIDADG family rather than reverse transcriptases. Such coincidences suggest causal relationships between the shift to DNA-based mobility, the loss of one of the two ribozyme sites for binding the 59 exon, and the exclusive use of hydrolysis to initiate splicing.

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A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis

Cited by 261 publications

References 40 publications

Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes

Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes

Ectomycorrhizal communities of Quercus garryana are similar on serpentine and nonserpentine soils

Recurrent insertion of 5′-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs

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