Rapid and reliable high‐throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms

Dentinger, Bryn T. M.; Margaritescu, Simona; Moncalvo, Jean‐Marc

doi:10.1111/j.1755-0998.2009.02825.x

Cited by 114 publications

(65 citation statements)

References 17 publications

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“…Partial sequences of the nuclear ribosomal internal transcribed spacers (nrITS) and nuclear ribosomal large subunit (nrLSU) were amplified by PCR using the primer pairs ITS8F-ITS6R (Dentinger et al 2010) and LR0R-LR7 (Vilgalys and Hester 1990), respectively and following the cycling conditions in the original publications. PCR products were purified using 2 units of Exonuclease I (Thermo Fisher Scientifics) and 1 U FastAP Thermosensitive Alkaline Phosphatase (Thermo Fisher Scientifics) per 1 µl of PCR product, incubated at 37 °C for 15 min, followed by denaturing at 85 °C for 15 min.…”

Section: Methodsmentioning

confidence: 99%

Reclassification of Parapterulicium Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of Baltazaria gen. nov.

Leal-Dutra¹,

Neves²,

Griffith³

et al. 2018

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The genus Parapterulicium was first introduced to accommodate two Brazilian species of coralloid fungi with affinities to Pterulaceae (Agaricales). Despite the coralloid habit and the presence of skeletal hyphae, other features, notably the presence of gloeocystidia, dichophyses and papillate hyphal ends, differentiate this genus from Pterulaceaesensu stricto. Fieldwork in Brazil resulted in the rediscovery of two coralloid fungi identifiable as Parapterulicium, the first verified collections of this genus since Corner’s original work in the 1950s. Molecular phylogenetic analyses of nrITS and nrLSU sequences from these modern specimens revealed affinities with the /peniophorales clade in the Russulales, rather than Pterulaceae. The presence of distinctive hyphal elements, homologous to the defining features of /peniophorales, is consistent with the phylogenetic evidence and thus clearly distinguished Parapterulicium and its type species P.subarbusculum from Pterulaceae, placing this genus within /peniophorales. Parapterulicium was also found to be polyphyletic so Baltazaria gen. nov. is proposed to accommodate P.octopodites, Scytinostromagalactinum, S.neogalactinum and S.eurasiaticogalactinum also within /peniophorales.

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Section: Methodsmentioning

confidence: 99%

Reclassification of Parapterulicium Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of Baltazaria gen. nov.

Leal-Dutra¹,

Neves²,

Griffith³

et al. 2018

Self Cite

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“…In most cases, fresh specimens are morphologically identified to generate the barcode sequences (Dentinger et al . ; Steinke & Hanner ). However, generating DNA barcodes from museum voucher specimens were realized in past decades (Van Houdt et al .…”

Section: Introductionmentioning

confidence: 99%

Design of Mini‐barcode for Catfishes for assessment of archival biodiversity

Bhattacharjee

Ghosh

2013

Molecular Ecology Resources

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Recovery of DNA barcode sequences is often challenging from the archived specimens. However, short fragments of DNA may be recovered, which would significantly improve many unresolved taxonomic conflicts. Here, we designed a mini-barcode for catfishes comprising several species and many cryptic taxa. We analysed a data set of 3048 publicly available COI barcode sequences representing 547 worldwide catfish species and performed 152 628 interspecies comparisons. A significantly more positively correlated interspecies distance was detected with transversion (0.78, P < 0.001) than with transition (0.70, P < 0.001). This suggested that transversions were better diagnostics for species identification. In the aligned data set, two transversion-rich fragments (53 bp and 119 bp) were identified. Transition/transversion bias value was 1.04 in 53-bp fragment, 1.23 in 119-bp fragment and 1.50 in full-length barcode. The interspecies distance with full-length barcode was 0.212 ± 0.037, while that with 53-bp and 119-bp fragments was 0.325 ± 0.039 and 0.218 ± 0.045, respectively. Survey of 53-bp fragment showed a possibility of only 1144 barcodes, while that of 119-bp fragment showed >4 million barcodes. Thus, the 119-bp fragment is a viable mini-barcode for catfishes comprising >3000 extant species. Experiment with 82 archived catfishes showed successful recovery of this mini-barcode using the designed primer. The mini-barcode sequences showed species-specific similarity in the range of 98-100% with the global database. Therefore, survey of a transversion-rich fragment within the full-length barcode would be an ideal approach of mini-barcode design for biodiversity assessment.

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“…Full nuclear ribosomal internal transcribed spacer nrITS (ITS1-5.8S-ITS2) and nuclear ribosomal large subunit (nrLSU) were PCR-amplified with primer pairs ITS6-R/ITS8-F, and the nuclear LSU rDNA (28S) were PCRamplified with LR0R/LR7 following Dentinger et al (2010) and Vilgalys & Hester (1990) respectively. Complementary unidirectional sequence reads were aligned and edited in Geneious 6.1.8 (Kearse et al 2012) and deposited in GenBank (Tab.…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Singerocomus atlanticus sp. nov., and a first record of Singerocomus rubriflavus (Boletaceae, Boletales) for Brazil

et al. 2018

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Ongoing surveys of macrofungi in the Brazilian Atlantic Forest ecoregion continue to uncover a diverse assemblage of ectomycorrhizal fungi. A new species of Boletaceae, Singerocomus atlanticus sp. nov., is described. Singerocomus rubrifl avus, previously known only from Guyana, is recorded for the fi rst time from the Brazilian Atlantic Forest. Phylogenetic data, macro-and microscopic illustrations, and comments are presented for each species.

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Rapid and reliable high‐throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms

Cited by 114 publications

References 17 publications

Reclassification of Parapterulicium Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of Baltazaria gen. nov.

Reclassification of Parapterulicium Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of Baltazaria gen. nov.

Design of Mini‐barcode for Catfishes for assessment of archival biodiversity

Singerocomus atlanticus sp. nov., and a first record of Singerocomus rubriflavus (Boletaceae, Boletales) for Brazil

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