Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae

Wanasinghe, Dhanushka N.; Phukhamsakda, Chayanard; Hyde, Kevin D.; Jeewon, Rajesh; Lee, Hyang Burm; Jones, E. B. Gareth; Tibpromma, Saowaluck; Tennakoon, Danushka S.; Dissanayake, Asha J.; Jayasiri, Subashini C.; Gafforov, Yusufjon; Camporesi, Erio; Bulgakov, Timur S.; Ekanayake, Anusha H.; Perera, Rekhani H.; Samarakoon, Milan C.; Goonasekara, Ishani D.; Mapook, Ausana; Li, Wenjing; Senanayake, Indunil C.; Li, Junfu; Norphanphoun, Chada; Doilom, Mingkwan; Bahkali, Ali H.; Xu, Jianchu; Mortimer, Peter E.; Tibell, Leif; Tibell, Sanja; Karunarathna, Samantha C.

doi:10.1007/s13225-018-0395-7

Cited by 206 publications

(245 citation statements)

References 208 publications

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“…The phylogenetic trees obtained from maximum likelihood were topologically congruent to previous studies on Phaeosphaeriaceae (Phookamsak et al 2014; Thambugala et al 2014; Tennakoon et al 2016; Karunarathna et al 2017; Wanasinghe et al 2018). This phylogenetic analysis showed the placement of 45 genera within Phaeosphaeriaceae.…”

Section: Resultssupporting

confidence: 83%

“…In addition, representatives of the Phaeosphaeriaceae were selected following Tennakoon et al (2016) and Wanasinghe et al (2018) (Table 1). Combined multi-locus sequence data of ITS, LSU, SSU and tef1 regions were aligned using default settings of MAFFT v.7 (Katoh et al 2017) and manually adjusted using BioEdit 7.1.3 (Hall 1999) to allow maximum alignment and minimum gaps.…”

Section: Methodsmentioning

confidence: 99%

“…Phaeosphaeriaceae is a highly diverse and large family in the order Pleosporales (Hyde et al 2013) with more than 42 accepted genera (Hyde et al 2017; Karunarathna et al 2017; Wanasinghe et al 2018). Members of Phaeosphaeriaceae are pathogens or hyper-parasites on living plants and humans and saprobes of decaying plant matter (Tennakoon et al 2016; Ahmed et al 2017).…”

Section: Introductionmentioning

confidence: 99%

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Sulcispora supratumida sp. nov. (Phaeosphaeriaceae, Pleosporales) on Anthoxanthum odoratum from Italy

Senanayake

Jeewon

Camporesi³

et al. 2018

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Sulcispora is typified by S.pleurospora. We collected a sulcispora-like taxon on leaves of Anthoxanthumodoratum L. in Italy and obtained single ascospore isolates. Combined ITS, LSU, SSU and tef1 sequence analyses suggested that Sulcispora is placed in the family Phaeosphaeriaceae and a newly collected Sulcispora species is introduced here as S.supratumida sp. nov. Detailed descriptions and illustrations are provided for Sulcisporasupratumida and it is compared with the type species, S.pleurospora.

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Section: Resultssupporting

confidence: 83%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sulcispora supratumida sp. nov. (Phaeosphaeriaceae, Pleosporales) on Anthoxanthum odoratum from Italy

Senanayake

Jeewon

Camporesi³

et al. 2018

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“…Jeewon et al 2003Jeewon et al , 2017Ariyawansa et al 2015;Liu et al 2015;Hyde et al 2017a, b;Tibpromma et al 2017;Wanasinghe et al 2017Wanasinghe et al , 2018Jayawardena et al 2018a, b). The use of other molecular approaches based on DNA sequence data (e.g.…”

Section: Using Mgdna From Environment In Species Identificationmentioning

confidence: 99%

“…A combination of traditional characterization and molecular approaches has been used to identify and discover numerous novel species in recent years, e.g. Ariyawansa et al (2015), Liu et al (2015), Hyde et al (2016Hyde et al ( , 2017a, Li et al (2016), Tibpromma et al (2017), and Wanasinghe et al (2018). Targeting highly variable loci for distinguishing species has resulted in the discovery of cryptic species in molecular phylogenetic studies (Hebert et al 2003;Divakar et al 2016).…”

Section: Introductionmentioning

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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Marine Fungal Ecology in the Molecular Era

Sarma

Jeewon

2019

Advancing Frontiers in Mycology &Amp; Mycotechnology

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Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae

Cited by 206 publications

References 208 publications

Sulcispora supratumida sp. nov. (Phaeosphaeriaceae, Pleosporales) on Anthoxanthum odoratum from Italy

Sulcispora supratumida sp. nov. (Phaeosphaeriaceae, Pleosporales) on Anthoxanthum odoratum from Italy

Can we use environmental DNA as holotypes?

Marine Fungal Ecology in the Molecular Era

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