More Like this

1. Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals

   https://doi.org/10.1007/s13225-021-00480-y  

   Voigt, Kerstin; James, Timothy Y.; Kirk, Paul M.; Santiago, André L.; Waldman, Bruce; Griffith, Gareth W.; Fu, Minjie; Radek, Renate; Strassert, Jürgen F.; Wurzbacher, Christian; et al (July 2021, Fungal Diversity)

   Abstract The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in  Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota , Aphelidiomycota , Rozellomycota , Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga ( Chytridiomycota : Nephridiophagales ) , a new type species, Nephridiophaga blattellae , is proposed. 

   more » « less
2. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

   https://doi.org/10.3114/sim.2023.105.01  

   Groenewald, M.; Hittinger, C.T.; Bensch, K.; Opulente, D.A.; Shen, X.-X.; Li, Y.; Liu, C.; LaBella, A.L.; Zhou, X.; Limtong, S.; et al (May 2023, Studies in Mycology)

   The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina , it contains only one class compared to the 16 classes in Pezizomycotina . The third subphylum of Ascomycota , the Taphrinomycotina , consists of six classes and has approximately 10 times fewer species than the Saccharomycotina . These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families ( Lipomycetaceae , Trigonopsidaceae , Alloascoideaceae , Pichiaceae , Phaffomycetaceae , Saccharomycodaceae , and Saccharomycetaceae ), one comprises two current families ( Dipodascaceae and Trichomonascaceae ), one represents the genus Sporopachydermia , and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina , including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. 

   more » « less
3. Diploid-dominant life cycles characterize the early evolution of Fungi

   https://doi.org/10.1073/pnas.2116841119  

   Amses, Kevin R.; Simmons, D. Rabern; Longcore, Joyce E.; Mondo, Stephen J.; Seto, Kensuke; Jerônimo, Gustavo H.; Bonds, Anne E.; Quandt, C. Alisha; Davis, William J.; Chang, Ying; et al (September 2022, Proceedings of the National Academy of Sciences)

   Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane– and cell-wall–associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages. 

   more » « less
4. Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea

   https://doi.org/10.1111/mpp.13404  

   Singh, Ritu; Caseys, Celine; Kliebenstein, Daniel_J (December 2023, Molecular Plant Pathology)

   Abstract Botrytis cinereaPers. Fr. (teleomorph:Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity ofB. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combatB. cinerea. TaxonomyKingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus:Botrytis, species:cinerea. Host rangeB. cinereainfects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts ofB. cinerea. Genetic diversityThis polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PathogenicityGenetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. Disease control strategiesEfforts to controlB. cinerea, being a high‐diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology. 

   more » « less
5. Orders of Ascomycota

   https://doi.org/10.5943/mycosphere/16/1/8  

   Thiyagaraja, V; Hyde, KD; Piepenbring, M; Davydov, EA; Dai, DQ; Abdollahzadeh, J; Bundhun, D; Chethana, KWT; Crous, PW; Gajanayake, AJ; et al (May 2025, mycosphere)

   Ascomycota, the most speciose phylum of fungi, is a complex entity, comprising three diversesubphyla: Pezizomycotina, Saccharomycotina, and Taphrinomycotina. The largest and most diversesubphylum, Pezizomycotina, is a rich tapestry of 16 classes and 171 orders. Saccharomycotina, thesecond largest subphylum, is a diverse collection of seven classes and 12 orders, whileTaphrinomycotina, the smallest, is a unique assembly of six classes and six orders. Over the pastdecade, numerous taxonomic studies have focused on the generic, family, and class classifications ofAscomycota. These efforts, well-documented across various databases, are crucial for acomprehensive understanding of the classification. However, the study of taxonomy at the ordinallevel, a crucial tier in the taxonomic hierarchy, has been largely overlooked. In a global collaborationwith mycologists and lichenologists, this study presents the first comprehensive information on theorders within Pezizomycotina and Taphrinomycotina. The recent taxonomic classification ofSaccharomycotina has led to the exclusion of this subphylum from the present study, as an immediaterevision is not necessary. Each order is thoroughly discussed, highlighting its historical significance,current status, key identification characteristics, evolutionary relationships, ecological and economicroles, future recommendations, and updated family-level classification. Teaching diagrams for thelife cycles of several orders, viz. Asterinales, Helotiales, Hypocreales, Laboulbeniales, Meliolales,Mycosphaerellales, Ophiostomatales, Pezizales, Pleosporales, Phyllachorales, Rhytismatales,Sordariales, Venturiales, Xylariales (Pezizomycotina) and Pneumocystidales,Schizosaccharomycetales and Taphrinales (Taphrinomycotina) are provided. Each diagram is explained with a representative genus/genera of their sexual and asexual cycles of each order. WithinPezizomycotina, Dothideomycetes contains the highest number of orders, with 57, followed bySordariomycetes (52 orders), Lecanoromycetes (21 orders), Eurotiomycetes and Leotiomycetes (12orders each), Laboulbeniomycetes (3 orders), and Arthoniomycetes and Xylonomycetes (2 orderseach). Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Lichinomycetes, Orbiliomycetes,Pezizomycetes, Sareomycetes, and Xylobotryomycetes each contain a single order, whileThelocarpales and Vezdaeales are treated as incertae sedis within Pezizomycotina. Notably, theclasses Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Sareomycetes, andXylonomycetes, all recently grouped under Lichinomycetes, are treated as separate classes based onphylogenetic analysis and current literature. Within Lecanoromycetes, the synonymization ofSporastatiales with Rhizocarpales and Sarrameanales with Schaereriales is not supported in thephylogenetic analysis. These orders are retained separately, and the justifications are provided undereach section as well as in the discussion. Within Leotiomycetes, the order Medeolariales, which wasonce considered part of Helotiales, is treated as a distinct order based on phylogenetic evidence. Theclassification of Medeolariales may change as more data becomes available from different generegions. Lahmiales (Leotiomycetes) is not included in the phylogenetic analysis due to a lack ofmolecular data. Sareomycetes and Xylonomycetes are treated as separate classes. Spathulosporamixed with Lulworthiales and the inclusion of Spathulosporales within Lulworthiomycetidae issupported and extant molecular sampling is important to resolve the phylogenetic boundaries ofmembers of this subclass. The majority of the classes of Pezizomycotina and Taphrinomycotinaformed monophyletic clades in the phylogenetic analysis conducted based on SSU, LSU, 5.8S, TEFand RPB2 sequence data. However, Arthoniomycetes nested with the basal lineage ofDothideomycetes and formed a monophyletic clade also known as the superclass, Dothideomyceta.In Taphrinomycotina, a single order is accepted within each class. 

   more » « less