Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

Hibbett, David S.; Öhman, Anders; Glotzer, Dylan; Nuhn, Mitchell; Kirk, Paul M.; Nilsson, R. Henrik

doi:10.1016/j.fbr.2011.01.001

Cited by 310 publications

(247 citation statements)

References 46 publications

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“…Many fungal lineages do not seem to produce tangible fruiting bodies, and for those that do, the factors promoting -and acting against -fruiting body formation are only partly understood. As a result, most sampling sites and habitats host a much greater fungal diversity than the above-ground view offered by fruiting bodies would lead the observer to believe (Porter et al 2008;Hibbett et al 2011). Furthermore, discriminatory yet easily assessed morphological characters are something of a rare commodity in mycology, and morphology alone often falls short of providing unequivocal species identification and delimitation.…”

Section: Introductionmentioning

confidence: 99%

“…After all, ITS sequence data are available for a mere 1% of the hypothesized 1.5 million extant species of fungi (Hawksworth 2001;Hibbett et al 2011), and some newly generated sequences will be singletons, and perhaps look odd, for the reason that they have not been sequenced before, such that no fit objects of comparison are available. To routinely exclude sequences that differ from known sequences would obviously not be a good way to expand our knowledge of the fungal kingdom.…”

Section: Guideline 2 a Single Alignment Step Can Assess The Orientatmentioning

confidence: 99%

“…Taxonomic annotations should be verified before the sequences are used About half of the 250,000 public, full-length fungal ITS sequences are annotated to the level of species (Hibbett et al 2011). Several studies have, however, shown that the taxonomic reliability of the entries in the public sequence databases has yet to reach perfection, and more than 10% of the public fungal ITS sequences that carry a species name may in fact carry an incorrect species name (e.g., Nilsson et al 2006).…”

Section: Guideline 4 Sequences Can Be Broken In Other Puzzling Waysmentioning

confidence: 99%

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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson¹,

Tedersoo²,

Abarenkov³

et al. 2012

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Larsson K-H, Larsson E, Kõljalg U (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-63. doi: 10.3897/mycokeys.4.3606 Abstract Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contribut- Nilsson et al. / MycoKeys 4: 37-63 (2012) 38 ing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.

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Section: Introductionmentioning

confidence: 99%

Section: Guideline 2 a Single Alignment Step Can Assess The Orientatmentioning

confidence: 99%

Section: Guideline 4 Sequences Can Be Broken In Other Puzzling Waysmentioning

confidence: 99%

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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson¹,

Tedersoo²,

Abarenkov³

et al. 2012

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170

125

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“…According to Hibbett et al (2011) and Das and Deb, (2015), approximately 1.5 million fungi species exist in our environment, while (O'Brien, Parrent, Jackson, Moncalvo & Vilgalys, 2005) estimated that the species' richness ranges from 3.5 to 5.1 million.…”

Section: Introductionmentioning

confidence: 99%

Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: a Review

Fajarningsih

2016

Squalen Bull. Marine Fisheries Postharvest Biotech.

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Despite the fact that fungi are important sources of both bioactive compounds and mycotoxins, and that they are very ubiquitous in our environment, their species identification is hampered by incomplete and often unclear literature. Fungi identification is primarily based on their phenotypic and physiological characteristics. Nowadays, many molecular methods to identify fungal species have been developed. One of the methods considered as a new concept to rapidly and accurately identify unknown fungal sample is DNA Barcoding. This literature review will outline the use of DNA barcoding approach to rapidly identify fungal species and the use of ITS region that recently has been designated as primary DNA barcode for fungal kingdom. "DNA barcode" is a short, highly variable and standardized DNA region with approximately 700 nucleotides in length, which is used as a unique pattern to identify living things. Internal Transcribed Spacer (ITS) region of nuclear DNA (rDNA) has become the most sequenced region to identify fungal taxonomy at species level, and even within species. ITS region is a highly polymorphic noncoding region with enough taxonomic units. Therefore, it is able to separate sequences into species level. Even though ribosomal ITS as a universal barcode marker for fungi is still hampered by few limitations, the ITS will remain as the key choice for fungal identification. The search for alternative regions as DNA marker to improve fungal identification, especially in specific heredities, has already started.

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“…During the past decade, an increasingly large number of undescribed taxa within or related to Fungi have been detected, leading to the "dark matter fungi" concept (Hibbett et al, 2011;Jones et al, 2011;Kagami et al, 2014;Grossart et al, 2016;Yahr et al, 2016). This dark matter comprises a huge fungal diversity, widespread across different ecosystems, which have never been cultured, taxonomically classified or morphologically studied.…”

Section: Large Amount Of Novel Diversity Of Early-diverging Holomycotamentioning

confidence: 99%

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

et al. 2018

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Opisthokonta represents a major lineage of eukaryotes and includes fungi and metazoans, as well as other less known unicellular groups. The latter are paraphyletic assemblages that branch in between the former two groups, and thus are important for understanding the origin and early diversification of opisthokonts. The full range of their diversity, however, has not yet been explored from diverse ecological habitats. Freshwater environments are crucial sources for new diversity; they are considered even more heterogeneous than marine ecosystems. This heterogeneity implies more ecological niches where local eukaryotic communities are located. However, knowledge of the unicellular opisthokont diversity is scarce from freshwater environments. Here, we performed an 18S rDNA metabarcoding study in the Middle Paraná River, Argentina, to characterize the molecular diversity of microbial eukaryotes, in particular unicellular members of Opisthokonta. We identified a potential novel clade branching as a sister-group to Fungi. We also detected in our data that more than 60% operational taxonomic units classified as unicellular holozoans (animals and relatives) represent new taxa at the species level. Of the remaining, the majority was assigned to the newly described holozoan species, Syssomonas multiformis. Together, our results show that a large hidden diversity of unicellular members of opisthokonts still remain to be uncovered. We also found that the geographical and ecological distribution of several taxa considered exclusive to marine environments is wider than previously thought.

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Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

Cited by 310 publications

References 46 publications

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Internal Transcribed Spacer (ITS) as Dna Barcoding to Identify Fungal Species: a Review

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

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