From morphology to molecular biology: can we use sequence data to identify fungal endophytes?

Ko, Thida Win Ko; Stephenson, Steven L.; Bahkali, Ali H.; Hyde, Kevin D.

doi:10.1007/s13225-011-0130-0

Cited by 119 publications

(49 citation statements)

References 39 publications

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“…Many sequences deposited in GenBank are associated with erroneous taxon names (Nilsson et al 2006). While the quality and reliability of DNA sequences in public databases may be improving, some GenBank sequences may not be reliable, with as much as 86% of available fungal sequences not from the named organism (Ko Ko et al 2011). …”

Section: Discussionmentioning

confidence: 99%

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

et al. 2015

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Endophytes associated with crops have potential as beneficial inoculants in agriculture, but little is known about their genetic diversity and phylogenetic relationships. We carried out the first ever ecological and phylogenetic survey of the culturable fungal root endophytes of a wild barley species. Fungal root endophytes were isolated from 10 populations of wall barley (Hordeum murinum), and 112 taxa of fungi were identified based on internal transcribed spacer sequence similarity. We found representatives from 8 orders, 12 families and 18 genera. Within this group, only 34 isolates (30% of the total) could be confidently assigned to a species, and 23 of the isolates (21% of the total) had no significant match to anything deposited in GenBank (based on <85% sequence similarity). These results suggest a high proportion of novel fungi, with 28% not assigned to a known fungal order. This includes three endophytes that have been shown to significantly improve agronomic traits in cultivated barley. This study has, therefore, revealed a profound diversity of fungal root endophytes in a single wild relative of barley. Extrapolating from this, the study highlights the largely unknown, hugely diverse and potentially useful resource of crop wild relative endophytes.

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Section: Discussionmentioning

confidence: 99%

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

et al. 2015

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“…It is important to clarify relationships amongst Pestalotiopsis species as they are not only weak pathogens, but also prolific produces of novel medicinal compounds , Ko Ko et al 2011a, b, Xu et al 2010. Pestalotiopsis coffeae (Zimm) Y.X.…”

Section: Discussionmentioning

confidence: 99%

Two new species of Pestalotiopsis from Southern China

Song¹,

Kun²,

Hyde³

et al. 2013

Phytotaxa

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Three Pestalotiopsis isolates were obtained from leaves of Coffea arabica and Rhodomyrtus tomentosa. Among them, two isolates produced versicolorous conidia, and the other produced concolorous conidia. Phylogenetic analysis based on a combination of ITS, β-tubulin and tef1 gene sequence data clearly confirms that they belong to two species and distinguishes them from other species in this genus, with ex-type sequence data in GenBank. On the basis of evidence from morphology and molecular phylogeny they are described as new species, Pestalotiopsis coffeae-arabicae sp. nov. and P. rhodomyrtus sp. nov.

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“…Although this has been followed by numerous authors using ITS sequence data analysis, the use of ITS alone is not accurate (Promputtha et al 2005). Subsequent studies have shown that multi-gene analyses are needed to identify endophytes (Ko et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

Tibpromma¹,

Hyde²,

Bhat³

et al. 2018

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The authors established the taxonomic status of endophytic fungi associated with leaves of Pandanaceae collected from southern Thailand. Morphotypes were initially identified based on their characteristics in culture and species level identification was done based on both morphological characteristics and phylogenetic analyses of DNA sequence data. Twenty-two isolates from healthy leaves were categorised into eight morphotypes. Appropriate universal primers were used to amplify specific gene regions and phylogenetic analyses were performed to identify these endophytes and established relationships with extant fungi. The authors identified both ascomycete and basidiomycete species, including one new genus, seven new species and nine known species. Morphological descriptions, colour plates and phylogenies are given for each taxon. RESEARCH ARTICLESaowaluck Tibpromma et al. / MycoKeys 33: 25-67 (2018) 26

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From morphology to molecular biology: can we use sequence data to identify fungal endophytes?

Cited by 119 publications

References 39 publications

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

Two new species of Pestalotiopsis from Southern China

Identification of endophytic fungi from leaves of Pandanaceae based on their morphotypes and DNA sequence data from southern Thailand

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