Mycosphere Notes 102–168: Saprotrophic fungi on Vitis in China, Italy, Russia and Thailand

Jayawardena, Ruvishika S.; Hyde, Kevin D.; Chethana, K. W. Thilini; Daranagama, Dinushani A.; Dissanayake, Asha J.; Goonasekara, Ishani D.; Manawasinghe, Ishara S.; Mapook, Ausana; Jayasiri, Subashini C.; Karunarathna, Anuruddha; Li, C. G.; Phukhamsakda, Chayanard; Senanayake, Indunil C.; Wanasinghe, Dhanushka N.; Camporesi, Erio; Bulgakov, Timur S.; Li, X. H.; Liu, M.; Zhang, W.; Yan, Jun-Qing

doi:10.5943/mycosphere/9/1/1

Cited by 19 publications

(14 citation statements)

References 22 publications

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“…Thus, during the past decade, a polyphasic approach, employing multi-locus DNA data together with morphology and ecology, has been employed for species boundaries in the genus (Crous et al 2012, Udayanga et al 2014a, b, Huang et al 2015, Gao et al 2016, 2017, Guarnaccia and Crous 2017, 2018, Hyde et al 2017, 2018, Yang et al 2017a, b, 2018, Guarnaccia et al 2018, Jayawardena et al 2018, Perera et al 2018a, b, Tibpromma et al 2018, Wanasinghe et al 2018). …”

Section: Discussionmentioning

confidence: 99%

“…Although the classification of Diaporthe has been on-going, species are currently being identified based on a combination of morphological, cultural, phytopathological and phylogenetical analyses (Gomes et al 2013, Huang et al 2013, 2015, Udayanga et al 2014a, b, 2015, Fan et al 2015, Du et al 2016, Gao et al 2016, 2017, Guarnaccia and Crous 2017, Hyde et al 2017, 2018, Guarnaccia et al 2018, Jayawardena et al 2018, Perera et al 2018a, b, Tibpromma et al 2018, Wanasinghe et al 2018). However, fungi isolated from forest trees in China were recorded in old fungal literature without any living culture and molecular data (Teng 1963, Tai 1979, Wei 1979).…”

Section: Introductionmentioning

confidence: 99%

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High diversity of Diaporthe species associated with dieback diseases in China, with twelve new species described

2018

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Diaporthe species have often been reported as important plant pathogens, saprobes and endophytes on a wide range of plant hosts. Although several Diaporthe species have been recorded in China, little is known about species able to infect forest trees. Therefore, extensive surveys were recently conducted in Beijing, Heilongjiang, Jiangsu, Jiangxi, Shaanxi and Zhejiang Provinces. The current results emphasised on 15 species from 42 representative isolates involving 16 host genera using comparisons of DNA sequence data for the nuclear ribosomal internal transcribed spacer (ITS), calmodulin (cal), histone H3 (his3), partial translation elongation factor-1α (tef1) and β-tubulin (tub2) gene regions, as well as their morphological features. Three known species, D.biguttulata, D.eres and D.unshiuensis, were identified. In addition, twelve novel taxa were collected and are described as D.acerigena, D.alangii, D.betulina, D.caryae, D.cercidis, D.chensiensis, D.cinnamomi, D.conica, D.fraxinicola, D.kadsurae, D.padina and D.ukurunduensis. The current study improves the understanding of species causing diebacks on ecological and economic forest trees and provides useful information for the effective disease management of these hosts in China.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

High diversity of Diaporthe species associated with dieback diseases in China, with twelve new species described

2018

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“…Some recent identification of isolated taxa have incorporated analyses of ITS sequence data (Guo et al 2003;Promputtha et al 2007), Peregrine and Siddiqi (1972), Gonzalez and Tello (2011) Fungal Diversity Makovetz (1933), Stevenson and Wellman (1944), Mujica and Vergara (1945), Nasyrov (1964), Sarbhoy et al (1971), Pantidou (1973, Giatgong (1980), Bechet and Sapta-Forda (1981), Zhang (2003), Zhuang (2005) Whiteside (1966), Cook and Dubé (1989), Setati et al (2015), Michailides et al (2002), Kobayashi (2007), Vitale et al (2008), Bobev (2009), Casieri et al (2009, Gonzalez and Tello (2011), Dissanayake et al (2018), This study, Jayawardena et al (2018) Fungal Diversity Milholland (1994), Phillips (1998Phillips ( , 2000, Slippers et al Raabe et al (1981), Lee et al (1991), Mendes et al (1998), Holevas et al (2000), Phillips (2000), Gadgil (2005) C. fasciculatum Corda Cladosporiaceae Russia, Spain, Uzbekistan Gonzalez Fragoso (1921), Nagorny (1930) C. herbarum (Pers.) Link Cladosporiaceae P, E Fruit rot Australia,Chile, Spain …”

Section: Microfungi Collected From China Italy Russia and Thailandmentioning

confidence: 99%

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

et al. 2018

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This study is unique as it compares traditional and high-resolution culture-independent approaches using the same set of samples to study the saprotrophic fungi on Vitis vinifera. We identified the saprotrophic communities of table grape (Red Globe) and wine grape (Carbanate Gernischet) in China using both traditional and culture-independent techniques. The traditional approach used direct observations based on morphology, single spore isolation and phylogenetic analysis yielding 45 taxa which 19 were commonly detected in both cultivars. The same set of samples were then used for Illumina sequencing which analyzed ITS1 sequence data and detected 226 fungal OTUs, of which 176 and 189 belong to the cultivars Carbanate Gernischet and Red Globe, respectively. There were 139 OTUs shared between the two V. vinifera cultivars and 37 and 50 OTUs were specific to Carbanate Gernischet and Red Globe cultivars respectively. In the Carbanate Gernischet cultivar, Ascomycota accounted for 77% of the OTUs and in Red Globe, almost all sequenced were Ascomycota. The fungal taxa overlap at the genus and species level between the traditional and culture-independent approach was relatively low. In the traditional approach we were able to identify the taxa to species level, while in the culture-independent method we were frequently able to identify the taxa to family or genus level. This is remarkable as we used the same set of samples collected in China for both approaches. We recommend the use of traditional techniques to accurately identify taxa. Culture-independent method can be used to get a better understanding about the organisms that are present in a host in its natural environment. We identified primary and secondary plant pathogens and endophytes in the saprotrophic fungal communities, which support previous observations, that dead plant material in grape vineyards can be the primary sources of disease. Finally, based on present and previous findings, we provide a worldwide checklist of 905 fungal taxa on Vitis species, which includes their mode of life and distribution.

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“…In their study using multigene analyses the species were identified. ITS sequence data alone can be used in identification to genus or the species complex levels (Jayawardena et al , 2018a, but it has insufficient information to provide a better resolution at species or below species level.…”

Section: Colletotrichum Cordamentioning

confidence: 99%

“…OTUs could be assigned to species complexes but phylogenetic placement was ambiguous hence the reliability of the ITS is being questioned. For a better resolution of this genus protein coding gene regions are required (Jayawardena et al 2018a) but how far are we going to favour the use of alternative genes should we be dealing with OTUs suspected to be plant pathogens for a stable classification and appropriate nomenclature.…”

Section: Colletotrichum Cordamentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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Mycosphere Notes 102–168: Saprotrophic fungi on Vitis in China, Italy, Russia and Thailand

Cited by 19 publications

References 22 publications

High diversity of Diaporthe species associated with dieback diseases in China, with twelve new species described

High diversity of Diaporthe species associated with dieback diseases in China, with twelve new species described

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

Can we use environmental DNA as holotypes?

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