Rare or rarely detected? Ceraceosorus guamensis sp. nov.: a second described species of Ceraceosorales and the potential for underdetection of rare lineages with common sampling techniques

Kijpornyongpan, Teeratas; Aime, M. Catherine

doi:10.1007/s10482-016-0715-4

Cited by 20 publications

(22 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A growing number of studies is challenging the utility of ITS for delimiting, recognizing and identifying fungal species in certain lineages (O'Donnell and Cigelnik 1997 ; Nilsson et al 2008 ; Bellemain et al 2010 ; Pino-Bodas et al 2013 ; Kijpornyongpan and Aime 2016 ; Thiery et al 2016 ; Hughes et al 2018 ; Kruse et al 2018a , b ; Parks et al 2019 ; Tremble et al 2019 ; Stadler et al 2020 ). A minor problem is that ITS may not amplify in all fungi (Kijpornyongpan and Aime 2016 ), but sequencing success is better than with many other markers (Schoch et al 2012 ). More important caveats include lack of resolution and the potential presence of non-homologous ITS copies in the genome.…”

Section: Caveats Of the Its As Universal Dna Barcoding Marker In Fungmentioning

confidence: 99%

“…Wörheide et al 2004 ; Rosselló et al 2006 ; Stewart and Cavanaugh 2007 ). There is also growing evidence in certain fungal lineages (Smith et al 2007 ; Simon and Weiß 2008 ; Lindner and Banik 2011 ; Kiss 2012 ; Vydryakova et al 2012 ; Wilson et al 2012 ; Harrington et al 2014 ; Li et al 2013 , 2017 ; Kijpornyongpan and Aime 2016 ; McTaggart and Aime 2018 ; Colabella et al 2018 ; Heeger et al 2018 ; Hughes et al 2018 ; Stadler et al 2020 ). In most fungi, however, the rDNA cistron, including the ITS, appears to follow the principle of concerted evolution (Ganley and Kobayashi 2007 ).…”

Section: Caveats Of the Its As Universal Dna Barcoding Marker In Fungmentioning

confidence: 99%

See 1 more Smart Citation

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

et al. 2020

View full text Add to dashboard Cite

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

show abstract

Section: Caveats Of the Its As Universal Dna Barcoding Marker In Fungmentioning

confidence: 99%

Section: Caveats Of the Its As Universal Dna Barcoding Marker In Fungmentioning

confidence: 99%

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The situation is further complicated by the potential presence of multiple divergent ITS copies within genomes of one species, or, as shown by Peršoh et al (2009) and Stadler et al (2014a) , even among single spore isolates from the same perithecium in a heterokaryotic setting. Such variations may be due to degenerate copies ( Won & Renner 2005 , Harpke & Peterson 2008 ), failure to converge into a single canonical ITS version ( Li et al 2013 ), potentially with multiple polymorphic positions, or the maintenance of multiple rDNA cistrons ( Ko & Jung 2002 , Wörheide et al 2004 , Lindner & Banik 2010, Harrington et al 2014 , Kijpornyongpan & Aime 2016 ). All of these issues are prone to produce artefact “shadow taxa” if a barcode sequence were sufficient to serve as the type for a species.…”

Section: Ten Reasonsmentioning

confidence: 99%

Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon

et al. 2018

View full text Add to dashboard Cite

Abstract:The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.

show abstract

“…Most of the South Pacific islands remain under-explored for fungi, although these also appear rich in rare and endemic taxa (e.g. Kijpornyongpan and Aime 2016). Importantly, newly discovered taxa from rare lineages were shown to harbour the majority of novel genes in comparative genomic studies in smut fungi (Kijpornyongpan et al 2018), highlighting the urgency in documenting this diversity before it disappears.…”

Section: Discussionmentioning

confidence: 99%

A new species of Cintractiella (Ustilaginales) from the volcanic island of Kosrae, Caroline Islands, Micronesia

Aime

Kijpornyongpan

Abbasi

et al. 2018

Self Cite

View full text Add to dashboard Cite

Cintractiella is an unusual genus of smut fungi containing two described species that produce sori as adventitious gall-like spikelets on members of tribe Hypolytreae (subfam. Mapanioideae, Cyperaceae). In September 200, during a botanical expedition on the volcanic island of Kosrae located in the eastern Caroline Islands and within the Federated States of Micronesia, a specimen of Mapaniapacifica was collected displaying Cintractiella-like sori in adventitious spikelets on the host leaves. Sori were hypophyllous, occurring in groups of spikelets composed of olivaceous-brown scale-like leaves, 1–1.5 mm wide and up to 6 mm long. Microscopic comparison with the protologue and drawings of the type material of C.lamii show several differences in teliospore and sori characters between it and the newly collected material on Mapania. To our knowledge, this represents only the second known collection of any member of Cintractiella on vegetative organs of Hypolytreae and a third species for this genus and the only known smut species infecting Mapania, herein described as Cintractiellakosraensissp. nov.

show abstract

Rare or rarely detected? Ceraceosorus guamensis sp. nov.: a second described species of Ceraceosorales and the potential for underdetection of rare lineages with common sampling techniques

Cited by 20 publications

References 57 publications

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon

A new species of Cintractiella (Ustilaginales) from the volcanic island of Kosrae, Caroline Islands, Micronesia

Contact Info

Product

Resources

About