Glomeromycota rRNA genes?the diversity of myths?

Schüßler, Arthur; Schwarzott, Daniel; Walker, Christopher

doi:10.1007/s00572-003-0250-9

Cited by 17 publications

(16 citation statements)

References 4 publications

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“…Such morphological diversity is not impossible, as both acaulosporoid and glomoid spores were demonstrated to form in the genus Ambispora (Walker et al ., 2007). However, as a parsimonious explanation it is also possible that the short sequences reported as those of O. bareai could have been derived from xenobiotic DNA (Schüßler et al ., 2003) of a Diversispora sp. present in the mixed trap pot culture.…”

Section: Discussionmentioning

confidence: 99%

“…The suitability of molecular genetic markers for comprehensive ecological community sampling can be compromised either by inadequate taxon resolution, for example as a result of DNA sequence conservation, or by failure to detect lineages, for example as a result of selectivity of PCR primers (Schüßler et al ., 2001a; Walker et al ., 2007). To address such problems, more reliable and comprehensive sequence databases are needed that are based on accurately identified organisms (Schüßler et al ., 2003; Vilgalys, 2003; Bidartondo et al ., 2008; Nilsson et al ., 2008).…”

Section: Introductionmentioning

confidence: 99%

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Diversispora celata sp. nov: molecular ecology and phylotaxonomy of an inconspicuous arbuscular mycorrhizal fungus

2009

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Summary• The increasing numbers of taxonomically unassigned phylotypes reported in molecular ecological studies contrast with the few formally described arbuscular mycorrhizal fungi (AMF; Glomeromycota). Here, a species new to science with Glomus-like spores is phylogenetically, morphologically and ecologically characterized.• From single spore isolates of a previously recognized member of the Diversisporaceae from Swiss agricultural grassland, 17 new nuclear internal transcribed spacer (ITS), large subunit (LSU) and small subunit (SSU) ribosomal RNA (rRNA) gene sequences were determined and compared with 14 newly generated sequences of two close relatives and public database sequences, including environmental sequences, of known geographic origin.• SSU ribosomal DNA (rDNA) sequence signatures and phylogenies based on ITS, LSU and SSU rDNA sequences show that the fungus belongs to the genus Diversispora. It is described as Diversispora celata sp. nov. Comparison with environmental sequences in the public domain confirmed its molecular genetic distinctiveness and revealed a cross-continental distribution of close relatives.• The value of combining morphology and phylogeny to characterize AMF was reinforced by the morphological similarity to other species and the inconspicuous nature of D. celata spores and mycorrhizas. Inclusion of all three nuclear rDNA regions in species descriptions will facilitate species determination from environmental phylotypes.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Diversispora celata sp. nov: molecular ecology and phylotaxonomy of an inconspicuous arbuscular mycorrhizal fungus

2009

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“…To accurately identify the obtained AMF OTUs, the representative sequence for each OTU was queried against the Krüger et al (2012) database using the BLAST algorithm. This curated database was used as public databases such as GenBank may contain sequences of incorrectly identified AMF isolates (Schüssler et al, 2003;Bidartondo, 2008). In contrast, the Krüger et al (2012) database contains high-quality sequences, obtained from well characterized isolates according to the taxonomy of Schüßler and Walker (2010).…”

Section: Its1 Its2mentioning

confidence: 99%

Evaluation of six primer pairs targeting the nuclear rRNA operon for characterization of arbuscular mycorrhizal fungal (AMF) communities using 454 pyrosequencing

Geel

Busschaert

Honnay

et al. 2014

Journal of Microbiological Methods

137

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“…Indeed, contemporary scientific literature is strewn with cases of mistaken species identities resulting from compromised DNA sequence comparison [10], [12]–[13].…”

Section: Introductionmentioning

confidence: 99%

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

et al. 2006

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BackgroundDNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries.Methodology/Principal FindingsThe present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations.ConclusionsThe problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.

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Glomeromycota rRNA genes?the diversity of myths?

Cited by 17 publications

References 4 publications

Diversispora celata sp. nov: molecular ecology and phylotaxonomy of an inconspicuous arbuscular mycorrhizal fungus

Diversispora celata sp. nov: molecular ecology and phylotaxonomy of an inconspicuous arbuscular mycorrhizal fungus

Evaluation of six primer pairs targeting the nuclear rRNA operon for characterization of arbuscular mycorrhizal fungal (AMF) communities using 454 pyrosequencing

Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

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