Six simple guidelines for introducing new genera of fungi

Aspergillus is one of the economically most important fungal genera. Recently, the ICN adopted the single name nomenclature which has forced mycologists to choose one name for fungi (e.g. Aspergillus, Fusarium, Penicillium, etc.). Previously two proposals for the single name nomenclature in Aspergillus were presented: one attributes the name “Aspergillus” to clades comprising seven different teleomorphic names, by supporting the monophyly of this genus; the other proposes that Aspergillus is a non-monophyletic genus, by preserving the Aspergillus name only to species belonging to subgenus Circumdati and maintaining the sexual names in the other clades. The aim of our study was to test the monophyly of Aspergilli by two independent phylogenetic analyses using a multilocus phylogenetic approach. One test was run on the publicly available coding regions of six genes (RPB1, RPB2, Tsr1, Cct8, BenA, CaM), using 96 species of Penicillium, Aspergillus and related taxa. Bayesian (MrBayes) and Ultrafast Maximum Likelihood (IQ-Tree) and Rapid Maximum Likelihood (RaxML) analyses gave the same conclusion highly supporting the monophyly of Aspergillus. The other analyses were also performed by using publicly available data of the coding sequences of nine loci (18S rRNA, 5,8S rRNA, 28S rRNA (D1-D2), RPB1, RPB2, CaM, BenA, Tsr1, Cct8) of 204 different species. Both Bayesian (MrBayes) and Maximum Likelihood (RAxML) trees obtained by this second round of independent analyses strongly supported the monophyly of the genus Aspergillus. The stability test also confirmed the robustness of the results obtained. In conclusion, statistical analyses have rejected the hypothesis that the Aspergilli are non-monophyletic, and provided robust arguments that the genus is monophyletic and clearly separated from the monophyletic genus Penicillium. There is no phylogenetic evidence to split Aspergillus into several genera and the name Aspergillus can be used for all the species belonging to Aspergillus i.e. the clade comprising the subgenera Aspergillus, Circumdati, Fumigati, Nidulantes, section Cremei and certain species which were formerly part of the genera Phialosimplex and Polypaecilum. Section Cremei and the clade containing Polypaecilum and Phialosimplex are proposed as new subgenera of Aspergillus. The phylogenetic analysis also clearly shows that Aspergillus clavatoflavus and A. zonatus do not belong to the genus Aspergillus. Aspergillus clavatoflavus is therefore transferred to a new genus Aspergillago as Aspergillago clavatoflavus and A. zonatus was transferred to Penicilliopsis as P. zonata. The subgenera of Aspergillus share similar extrolite profiles indicating that the genus is one large genus from a chemotaxonomical point of view. Morphological and ecophysiological characteristics of the species also strongly indicate that Aspergillus is a polythetic class in phenotypic characters.

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“…(2016) could be retrieved from the recently guidelines published on IMA Fungus for introducing new genera of fungi (Vellinga et al. 2015).…”

Section: Discussionmentioning

confidence: 99%

Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles

Kocsubé¹,

Perrone²,

Magistà³

et al. 2016

Studies in Mycology

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“…The recent cascade of phylogenetic studies that propose changing species and genus concepts involving many species recombinations due to an often exagerated splitting of the traditional genera into smaller satellite genera (see Vellinga et al 2015), is rapidly becoming a burden to all users of taxonomic information (Garnett and Christidis 2017). The flood of newly recognized genera for wellknown species is not only discouraging, it poses unsurmountable problems for part of the amateur mycological community in Europe.…”

Section: The Growing Implication Of Citizen Sciencists In Sequence-bamentioning

confidence: 99%

The unbearable lightness of sequenced-based identification

Hofstetter

Buyck

Eyssartier³

et al. 2019

Fungal Diversity

109

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Using the basic GenBank local alignment search tool program (BLAST) to identify fungi collected in a recently protected beech forest at Montricher (Switzerland), the number of ITS sequences associated to the wrong taxon name appears to be around 30%, even higher than previously estimated. Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected, viz. first records for Switzerland, rare or patrimonial species and problematic species (when BLAST top scores were equally high for different species), all belonging to Agaricomycotina. This paper dissects for the first time a number of sequence-based identifications, thereby showing in every detail-particularly to the user community of taxonomic information-why sequence-based identification in the context of a fungal inventory can easily go wrong. Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories: we spent two months on verification of approx. 20 identifications. Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification, it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata. While checking the original publications associated with top score sequences for the few examples that were here reexamined , a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank. Advantages and pitfalls of sequence-based identification are discussed, particularly in the light of undertaking fungal inventories. Recommendations are made to avoid or reduce some of the major problems with sequence-based identification. Nevertheless, the prospects for a more reliable sequence-based identification of fungi remain quite dim, unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.

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“…Mollisia are uncommon and an apothecium-centric approach has resulted in the neglect of potentially taxonomically informative asexual state characters (but see: Le Gal and Mangenot 1956, 1961, Aebi 1972, Tanney et al 2016a). Tanney (Vellinga et al 2015). As sampling increases and patterns emerge, this option would eventually capitulate to the division of a broad Mollisia genus, favouring more informative and monophyletic generic concepts.…”

Section: Taxonomic Issues and Solutionsmentioning

confidence: 99%

“…: a monophyletic clade comprising several species sharing distinct characters. A taxonomic upheaval in this lineage is likely in the horizon; being parsimonious with name changes and mindful of guidelines for introducing new genera presented by Vellinga et al (2015) will ensure a more stable, user-friendly taxonomic system. Forest Region of Eastern Canada has proven itself to be a rich source of biodiversity that has the potential to deliver environmentally sustainable pest management practises.…”

Section: Taxonomic Issues and Solutionsmentioning

confidence: 99%

“…: Gams et al 2005). In their guidelines for introducing new fungal genera, Vellinga et al (2015) recommended that all recognized genera be monophyletic, not only those that are the focus of a particular study. This presents a challenge for large, undersampled polyphyletic genera such as Lophodermium, which effectively spans the family Rhytismataceae.…”

Section: Rhytismataceaementioning

confidence: 99%

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A Taxonomic and Phylogenetic Investigation of Conifer Endophytes of Eastern Canada

Tanney¹

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Research interest in endophytic fungi has increased substantially, yet is the current research paradigm capable of addressing fundamental taxonomic questions?More than half of the ca. 30,000 endophyte sequences accessioned into GenBank are unidentified to the family rank and this disparity grows every year. The problems with identifying endophytes are a lack of taxonomically informative morphological characters in vitro and a paucity of relevant DNA reference sequences. A study involving ca. 2,600Picea endophyte cultures from the Acadian Forest Region in Eastern Canada sought to address these taxonomic issues with a combined approach involving molecular methods, classical taxonomy, and field work. It was hypothesized that foliar endophytes have complex life histories involving saprotrophic reproductive stages associated with the host foliage, alternative host substrates, or alternate hosts. Based on inferences from phylogenetic data, new field collections or herbarium specimens were sought to connect unidentifiable endophytes with identifiable material. Approximately 40 endophytes were connected with identifiable material, which resulted in the description of four novel genera and 21 novel species and substantial progress in endophyte taxonomy. Endophytes were connected with saprotrophs and exhibited reproductive stages on non-foliar tissues or different hosts. These results provide support for the foraging ascomycete hypothesis, postulating that for some fungi endophytism is a secondary life history strategy that facilitates persistence and dispersal in the absence of a primary host. This thesis provides an alternate approach to identifying endophytes by considering the whole fungus interacting within its natural habitat.iii Acknowledgements I would first like to thank my supervisor Dr. Keith A. Seifert for providing me with the freedom and support to conduct the research presented in this thesis as well as many other side projects and curiosities. Keith generously provided many opportunities to travel to domestic and international conferences, which made me more aware of the directions of global mycological research and provided the opportunity to meet many of the great mycological heroes and their contemporaries. Our discussions over the last five years have contributed to my development as a more well-rounded and openminded researcher, professional, and person; his honesty and integrity are qualities that all professionals should aspire to have. I am indebted to Keith for the knowledge, experience, and personal growth I gained over the last five years in his lab. I thank Dr. J. David Miller for providing stimulating discourse, travel and collecting opportunities, and of course the unique opportunity to work on this project, which proved to be an exciting and captivating experience. I hope that we can continue collaborating on this and other projects in the near future. Myron Smith provided support and advice throughout this process. The Carleton University Graduate Administrators Darlene Moss and Lisa Chiarel...

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Six simple guidelines for introducing new genera of fungi

Cited by 53 publications

References 30 publications

Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles

Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles

The unbearable lightness of sequenced-based identification

A Taxonomic and Phylogenetic Investigation of Conifer Endophytes of Eastern Canada

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