Studies in Mycology最新文献

{"title":"What are the 100 most cited fungal genera?","authors":"C S Bhunjun, Y J Chen, C Phukhamsakda, T Boekhout, J Z Groenewald, E H C McKenzie, E C Francisco, J C Frisvad, M Groenewald, V G Hurdeal, J Luangsa-Ard, G Perrone, C M Visagie, F Y Bai, J Błaszkowski, U Braun, F A de Souza, M B de Queiroz, A K Dutta, D Gonkhom, B T Goto, V Guarnaccia, F Hagen, J Houbraken, M A Lachance, J J Li, K Y Luo, F Magurno, S Mongkolsamrit, V Robert, N Roy, S Tibpromma, D N Wanasinghe, D Q Wang, D P Wei, C L Zhao, W Aiphuk, O Ajayi-Oyetunde, T D Arantes, J C Araujo, D Begerow, M Bakhshi, R N Barbosa, F H Behrens, K Bensch, J D P Bezerra, P Bilański, C A Bradley, B Bubner, T I Burgess, B Buyck, N Čadež, L Cai, F J S Calaça, L J Campbell, P Chaverri, Y Y Chen, K W T Chethana, B Coetzee, M M Costa, Q Chen, F A Custódio, Y C Dai, U Damm, A L C M A Santiago, R M De Miccolis Angelini, J Dijksterhuis, A J Dissanayake, M Doilom, W Dong, E Álvarez-Duarte, M Fischer, A J Gajanayake, J Gené, D Gomdola, A A M Gomes, G Hausner, M Q He, L Hou, I Iturrieta-González, F Jami, R Jankowiak, R S Jayawardena, H Kandemir, L Kiss, N Kobmoo, T Kowalski, L Landi, C G Lin, J K Liu, X B Liu, M Loizides, T Luangharn, S S N Maharachchikumbura, G J Makhathini Mkhwanazi, I S Manawasinghe, Y Marin-Felix, A R McTaggart, P A Moreau, O V Morozova, L Mostert, H D Osiewacz, D Pem, R Phookamsak, S Pollastro, A Pordel, C Poyntner, A J L Phillips, M Phonemany, I Promputtha, A R Rathnayaka, A M Rodrigues, G Romanazzi, L Rothmann, C Salgado-Salazar, M Sandoval-Denis, S J Saupe, M Scholler, P Scott, R G Shivas, P Silar, A G S Silva-Filho, C M Souza-Motta, C F J Spies, A M Stchigel, K Sterflinger, R C Summerbell, T Y Svetasheva, S Takamatsu, B Theelen, R C Theodoro, M Thines, N Thongklang, R Torres, B Turchetti, T van den Brule, X W Wang, F Wartchow, S Welti, S N Wijesinghe, F Wu, R Xu, Z L Yang, N Yilmaz, A Yurkov, L Zhao, R L Zhao, N Zhou, K D Hyde, P W Crous","doi":"10.3114/sim.2024.108.01","DOIUrl":"10.3114/sim.2024.108.01","url":null,"abstract":"<p><p>The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are <i>Saccharomyces</i>, <i>Candida</i>, <i>Aspergillus</i>, <i>Fusarium</i>, <i>Penicillium</i>, <i>Trichoderma</i>, <i>Botrytis</i>, <i>Pichia</i>, <i>Cryptococcus</i> and <i>Alternaria</i>. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. <b>Citation:</b> Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, T","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"108 ","pages":"1-411"},"PeriodicalIF":14.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11293126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Worldwide forest surveys reveal forty-three new species in <i>Phytophthora</i> major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity.","authors":"T Jung, I Milenković, Y Balci, J Janoušek, T Kudláček, Z Á Nagy, B Baharuddin, J Bakonyi, K D Broders, S O Cacciola, T-T Chang, N M Chi, T Corcobado, A Cravador, B Đorđević, A Durán, M Ferreira, C-H Fu, L Garcia, A Hieno, H-H Ho, C Hong, M Junaid, K Kageyama, T Kuswinanti, C Maia, T Májek, H Masuya, G Magnano di San Lio, B Mendieta-Araica, N Nasri, L S S Oliveira, A Pane, A Pérez-Sierra, A Rosmana, E Sanfuentes von Stowasser, B Scanu, R Singh, Z Stanivuković, M Tarigan, P Q Thu, Z Tomić, M Tomšovský, S Uematsu, J F Webber, H-C Zeng, F-C Zheng, C M Brasier, M Horta Jung","doi":"10.3114/sim.2024.107.04","DOIUrl":"https://doi.org/10.3114/sim.2024.107.04","url":null,"abstract":"&lt;p&gt;&lt;p&gt;During 25 surveys of global &lt;i&gt;Phytophthora&lt;/i&gt; diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of &lt;i&gt;Phytophthora&lt;/i&gt; major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels &lt;i&gt;ca&lt;/i&gt;. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the &lt;i&gt;Phytophthora&lt;/i&gt; clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single &lt;i&gt;Phytophthora&lt;/i&gt; clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in &lt;i&gt;Phytophthora&lt;/i&gt;. &lt;b&gt;Taxonomic novelties: New species:&lt;/b&gt; &lt;i&gt;Phytophthora amamensis&lt;/i&gt; T. Jung, K. Kageyama, H. Masuya & S. Uematsu, &lt;i&gt;Phytophthora angustata&lt;/i&gt; T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, &lt;i&gt;Phytophthora balkanensis&lt;/i&gt; I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, &lt;i&gt;Phytophthora borneensis&lt;/i&gt; T. Jung, A. Durán, M. Tarigan & M. Horta Jung, &lt;i&gt;Phytophthora calidophila&lt;/i&gt; T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, &lt;i&gt;Phytophthora catenulata&lt;/i&gt; T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, &lt;i&gt;Phytophthora celeris&lt;/i&gt; T. Jung, L. Oliveira, M. Tarigan & I. Milenković, &lt;i&gt;Phytophthora curvata&lt;/i&gt; T. Jung, A. Hieno, H. Masuya & M. ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"107 ","pages":"251-388"},"PeriodicalIF":16.5,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11003442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140871957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genus <i>Fomitopsis</i> (<i>Polyporales</i>, <i>Basidiomycota</i>) reconsidered.","authors":"V Spirin, K Runnel, J Vlasák, I Viner, M D Barrett, L Ryvarden, A Bernicchia, B Rivoire, A M Ainsworth, T Grebenc, M Cartabia, T Niemelä, K-H Larsson, O Miettinen","doi":"10.3114/sim.2024.107.03","DOIUrl":"https://doi.org/10.3114/sim.2024.107.03","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of &lt;i&gt;Fomitopsidaceae (Polyporales&lt;/i&gt;, &lt;i&gt;Basidiomycota)&lt;/i&gt;. After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, &lt;i&gt;viz&lt;/i&gt;. &lt;i&gt;Anthoporia&lt;/i&gt;, &lt;i&gt;Antrodia&lt;/i&gt; and &lt;i&gt;Fomitopsis&lt;/i&gt;. &lt;i&gt;Fomitopsis&lt;/i&gt; becomes a large genus with 128 accepted species, containing almost all former &lt;i&gt;Fomitopsis&lt;/i&gt; spp. and most species formerly placed in &lt;i&gt;Antrodia&lt;/i&gt;, &lt;i&gt;Daedalea&lt;/i&gt; and &lt;i&gt;Laccocephalum&lt;/i&gt;. Genera &lt;i&gt;Buglossoporus&lt;/i&gt;, &lt;i&gt;Cartilosoma&lt;/i&gt;, &lt;i&gt;Daedalea&lt;/i&gt;, &lt;i&gt;Melanoporia&lt;/i&gt;, &lt;i&gt;Neolentiporus&lt;/i&gt;, alongside twenty others, are treated as synonyms of &lt;i&gt;Fomitopsis&lt;/i&gt;. This generic scheme allows for morphologically distinct genera in &lt;i&gt;Fomitopsidaceae&lt;/i&gt;, unlike other schemes we considered. We provide arguments for retaining &lt;i&gt;Fomitopsis&lt;/i&gt; and suppressing earlier (&lt;i&gt;Daedalea&lt;/i&gt;, &lt;i&gt;Caloporus&lt;/i&gt;) or simultaneously published generic names (&lt;i&gt;Piptoporus&lt;/i&gt;) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + &lt;i&gt;TEF1&lt;/i&gt;, ITS + &lt;i&gt;TEF1&lt;/i&gt; + &lt;i&gt;RPB1&lt;/i&gt; and ITS + &lt;i&gt;TEF1&lt;/i&gt; + &lt;i&gt;RPB2&lt;/i&gt; datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided. &lt;b&gt;Taxonomic novelties: New species:&lt;/b&gt; &lt;i&gt;Fomitopsis algumicola&lt;/i&gt; Grebenc & Spirin, &lt;i&gt;F. caseosa&lt;/i&gt; Vlasák & Spirin, &lt;i&gt;F. cupressicola&lt;/i&gt; Vlasák, J. Vlasák Jr. & Spirin, &lt;i&gt;F. derelicta&lt;/i&gt; Vlasák & Spirin, &lt;i&gt;F. dollingeri&lt;/i&gt; Vlasák & Spirin, &lt;i&gt;F. fissa&lt;/i&gt; Vlasák & Spirin, &lt;i&gt;F. lapidosa&lt;/i&gt; Miettinen & Spirin, &lt;i&gt;F. lignicolor&lt;/i&gt; Vlasák & Spirin, &lt;i&gt;F. maculosa&lt;/i&gt; Miettinen & Spirin, &lt;i&gt;F. pannucea&lt;/i&gt; Runnel & Spirin, &lt;i&gt;F. perhiemata&lt;/i&gt; Viner & Spirin, &lt;i&gt;F. purpurea&lt;/i&gt; Spirin & Ryvarden, &lt;i&gt;F. retorrida&lt;/i&gt; Spirin & Kotiranta, &lt;i&gt;F. solaris&lt;/i&gt; Rivoire, A.M. Ainsworth & Vlasák, &lt;i&gt;F. tristis&lt;/i&gt; Miettinen & Spirin, &lt;i&gt;F. tunicata&lt;/i&gt; Miettinen & Spirin, &lt;i&gt;F. visenda&lt;/i&gt; Miettinen & Spirin. &lt;b&gt;New combinations:&lt;/b&gt; &lt;i&gt;Fomitopsis aculeata&lt;/i&gt; (Cooke) Spirin & Miettinen, &lt;i&gt;F. aethalodes&lt;/i&gt; (Mont.) Spirin, &lt;i&gt;F. alaskana&lt;/i&gt; (D.V. Baxter) Spirin & Vlasák, &lt;i&gt;F. albidoides&lt;/i&gt; (A. David & Dequatre) Bernicchia & Vlasák, &lt;i&gt;F. amygdalina&lt;/i&gt; (Berk. & Ravenel) Spirin & Vlasák, &lt;i&gt;F. angusta&lt;/i&gt; (Spirin & Vlasák) Spirin & Vlasák, &lt;i&gt;F. atypa&lt;/i&gt; (Lév.) Spirin & Vlasák, &lt;i&gt;F. caespitosa&lt;/i&gt; (Murrill) Spirin & Miettinen, &lt;i&gt;F. calcitrosa&lt;/i&gt; (Spirin & Miettinen) Spirin & Miettinen, &lt;i&gt;F. circularis&lt;/i&gt; (B.K. Cui & Hai J. Li) Spirin, &lt;i&gt;F. concentrica&lt;/i&gt; (G. Cunn.) M.D. Barrett, &lt;i&gt;F. cyclopis&lt;/i&gt; (Miettinen & Spirin) Miettinen & Spirin, &lt;i&gt;F. dickinsii&lt;/i&gt; (Berk. ex Cooke) Spirin, &lt;i&gt;F. elevata&lt;/i&gt; (Corner) Spirin & Miettinen, &lt;i&gt;F. eucalypti&lt;/i&gt; (Kalchbr.) Spirin, &lt;i","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"107 ","pages":"149-249"},"PeriodicalIF":16.5,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11003443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140868139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The subfamily <i>Xerocomoideae</i> (<i>Boletaceae</i>, <i>Boletales</i>) in China.","authors":"R Xue, X Zhang, C Xu, H J Xie, L L Wu, Y Wang, L P Tang, Y J Hao, K Zhao, S Jiang, Y Li, Y Y Yang, Z Li, Z Q Liang, N K Zeng","doi":"10.3114/sim.2023.106.03","DOIUrl":"10.3114/sim.2023.106.03","url":null,"abstract":"<p><p><i>Xerocomoideae</i> is an ecologically and economically important Boletaceae subfamily (<i>Boletales</i>) comprising 10 genera. Although many studies have focused on <i>Xerocomoideae</i> in China, the diversity, taxonomy and molecular phylogeny still remained incompletely understood. In the present study, taxonomic and phylogenetic studies on Chinese species of <i>Xerocomoideae</i> were carried out by morphological examinations and molecular phylogenetic analyses. Eight genera in <i>Xerocomoideae,</i> <i>viz.</i> <i>Aureoboletus,</i> <i>Boletellus,</i> <i>Heimioporus,</i> <i>Hemileccinum,</i> <i>Hourangia,</i> <i>Phylloporus,</i> <i>Pulchroboletus, and</i> <i>Xerocomus</i> were confirmed to be distributed in China; 97 species of the subfamily were accepted as being distributed in China; one ambiguous taxon was tentatively named <i>Bol. aff.</i> <i>putuoensis;</i> two synonyms, <i>viz.</i> <i>A. marroninus</i> and <i>P. dimorphus</i> were defined. Among the Chinese accepted species, 13 were newly described, <i>viz.</i> <i>A. albipes,</i> <i>A. conicus,</i> <i>A. ornatipes,</i> <i>Bol. erythrolepis, Bol. rubidus, Bol. sinochrysenteroides, Bol. subglobosus, Bol. zenghuoxingii,</i> <i>H. squamipes,</i> <i>P. hainanensis,</i> <i>Pul. erubescens,</i> <i>X. albotomentosus, and</i> <i>X. fuscatus, 36 known species were redescribed, and the other 48 species were reviewed. Keys to accepted species of</i> <i>Aureoboletus,</i> <i>Boletellus,</i> <i>Heimioporus,</i> <i>Hemileccinum,</i> <i>Hourangia,</i> <i>Phylloporus, and</i> <i>Xerocomus in China</i> were also provided. <b>Taxonomic novelties</b>: <b>New species</b>: <i>Aureoboletus albipes</i> N.K. Zeng, Xu Zhang & Zhi Q. Liang, <i>A. conicus</i> N.K. Zeng, Xu Zhang & Zhi Q. Liang, <i>A. ornatipes</i> N.K. Zeng, Xu Zhang & Zhi Q. Liang, <i>Boletellus erythrolepis</i> N.K. Zeng, R. Xue, S. Jiang & Zhi Q. Liang, <i>Bol. rubidus</i> N.K. Zeng, R. Xue, Y.J. Hao & Zhi Q. Liang, <i>Bol. sinochrysenteroides</i> N.K. Zeng, R. Xue & Kuan Zhao, <i>Bol. subglobosus</i> N.K. Zeng, R. Xue, S. Jiang & Zhi Q. Liang, <i>Bol. zenghuoxingii</i> N.K. Zeng, R. Xue, S. Jiang & Zhi Q. Liang, <i>Hemileccinum squamipes</i> N.K. Zeng, Chang Xu & Zhi Q. Liang, <i>Phylloporus hainanensis</i> N.K. Zeng, L.L. Wu, & Zhi Q. Liang, <i>Pulchroboletus erubescens</i> N.K. Zeng, Chang Xu & Zhi Q. Liang, <i>Xerocomus albotomentosus</i> N.K. Zeng, H.J. Xie, Chang Xu & Zhi Q. Liang, and <i>X. fuscatus</i> N.K. Zeng, H.J. Xie, Chang Xu & Zhi Q. Liang. <b>Citation</b>: Xue R, Zhang X, Xu C, Xie HJ, Wu LL, Wang Y, Tang LP, Hao YJ, Zhao K, Jiang S, Li Y, Yang YY, Li Z, Liang ZQ, Zeng NK (2023). The subfamily <i>Xerocomoideae</i> (<i>Boletaceae</i>, <i>Boletales</i>) in China. <i>Studies in Mycology</i> <b>106</b>: 95-197. doi: 10.3114/sim.2022.106.03.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"106 ","pages":"95-197"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New genera and species with chloridium-like morphotype in the <i>Chaetosphaeriales</i> and Vermiculariopsiellales.","authors":"M Réblová, J Nekvindová","doi":"10.3114/sim.2023.106.04","DOIUrl":"10.3114/sim.2023.106.04","url":null,"abstract":"&lt;p&gt;&lt;p&gt;In this study, we investigated the morphological and genetic variability of selected species belonging to the genus &lt;i&gt;Chloridium sensu lato&lt;/i&gt;, some also referred to as chloridium-like asexual morphs and other undescribed morphologically similar fungi. These species do not conform to the revised generic concept and thus necessitate a re-evaluation in terms of taxonomy and phylogeny. The family &lt;i&gt;Chaetosphaeriaceae&lt;/i&gt; (&lt;i&gt;Chaetosphaeriales&lt;/i&gt;) encompasses a wide range of asexual morphotypes, and among them, the simplest form is represented by &lt;i&gt;Chloridium&lt;/i&gt; sect. &lt;i&gt;Chloridium&lt;/i&gt;. The morphological simplicity of the &lt;i&gt;Chloridium&lt;/i&gt; morphotype has historically led to the amalgamation of numerous unrelated species, thereby creating a heterogeneous genus. By conducting phylogenetic reconstruction of four DNA loci and examining a set of 71 strains, including all available ex-type and other non-type strains as well as holotypes and other herbarium material, we were able to gain new insights into the relationships between these taxa. Phylogenetic analyses revealed that the studied species are distantly related to &lt;i&gt;Chloridium&lt;/i&gt; &lt;i&gt;sensu stricto&lt;/i&gt; and can be grouped into two orders in the &lt;i&gt;Sordariomycetes&lt;/i&gt;. Within the &lt;i&gt;Chaetosphaeriales&lt;/i&gt;, they formed nine well-separated genera in four clades, such as &lt;i&gt;Cacumisporium&lt;/i&gt;, &lt;i&gt;Caliciastrum gen. nov.&lt;/i&gt;, &lt;i&gt;Caligospora gen. nov.&lt;/i&gt;, &lt;i&gt;Capillisphaeria gen. nov.&lt;/i&gt;, &lt;i&gt;Curvichaeta&lt;/i&gt;, &lt;i&gt;Fusichloridium&lt;/i&gt;, &lt;i&gt;Geniculoseta gen. nov.&lt;/i&gt;, &lt;i&gt;Papillospora gen. nov.&lt;/i&gt;, and &lt;i&gt;Spicatispora gen. nov.&lt;/i&gt; We also established &lt;i&gt;Chloridiopsiella gen. nov.&lt;/i&gt; and &lt;i&gt;Chloridiopsis gen. nov.&lt;/i&gt; in &lt;i&gt;Vermiculariopsiellales&lt;/i&gt;. Four new species and eight new combinations are proposed in these genera. Our study provides a clearer understanding of the genus &lt;i&gt;Chloridium&lt;/i&gt;, its relationship to other morphologically similar fungi, and a new taxonomic treatment and molecular phylogeny to facilitate their accurate identification and classification in future research. &lt;b&gt;Taxonomic novelties:&lt;/b&gt; &lt;b&gt;New genera:&lt;/b&gt; &lt;i&gt;Caliciastrum&lt;/i&gt; Réblová, &lt;i&gt;Caligospora&lt;/i&gt; Réblová, &lt;i&gt;Capillisphaeria&lt;/i&gt; Réblová, &lt;i&gt;Chloridiopsiella&lt;/i&gt; Réblová, &lt;i&gt;Chloridiopsis&lt;/i&gt; Réblová, &lt;i&gt;Geniculoseta&lt;/i&gt; Réblová, &lt;i&gt;Papillospora&lt;/i&gt; Réblová, &lt;i&gt;Spicatispora&lt;/i&gt; Réblová; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Caliciastrum bicolor&lt;/i&gt; Réblová, &lt;i&gt;Caligospora pannosa&lt;/i&gt; Réblová, &lt;i&gt;Chloridiopsis syzygii&lt;/i&gt; Réblová, &lt;i&gt;Gongromerizella silvana&lt;/i&gt; Réblová; &lt;b&gt;New combinations:&lt;/b&gt; &lt;i&gt;Caligospora dilabens&lt;/i&gt; (Réblová & W. Gams) Réblová, &lt;i&gt;Capillisphaeria&lt;/i&gt; &lt;i&gt;crustacea&lt;/i&gt; (Sacc.) Réblová, &lt;i&gt;Chloridiopsiella preussii&lt;/i&gt; (W. Gams & Hol.-Jech.) Réblová, &lt;i&gt;Chloridiopsis constrictospora&lt;/i&gt; (Crous &lt;i&gt;et al&lt;/i&gt;.) Réblová, &lt;i&gt;Geniculoseta preussii&lt;/i&gt; (W. Gams & Hol.-Jech.) Réblová, &lt;i&gt;Papillospora hebetiseta&lt;/i&gt; (Réblová & W. Gams) Réblová, &lt;i&gt;Spicatispora carpatica&lt;/i&gt; (Hol.-Jech. & Révay) Réblová, &lt;i&gt;Spicatispora fennic","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":"199-258"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69600770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of <i>Microbotryomycetes</i>.","authors":"N Schoutteten, A Yurkov, O Leroux, D Haelewaters, D Van Der Straeten, O Miettinen, T Boekhout, D Begerow, A Verbeken","doi":"10.3114/sim.2023.106.02","DOIUrl":"10.3114/sim.2023.106.02","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;&lt;/b&gt; Mycoparasites in &lt;i&gt;Basidiomycota&lt;/i&gt; comprise a diverse group of fungi, both morphologically and phylogenetically. They interact with their hosts through either fusion-interaction or colacosome-interaction. Colacosomes are subcellular structures formed by the mycoparasite at the host-parasite interface, which penetrate the parasite and host cell walls. Previously, these structures were detected in 19 fungal species, usually by means of transmission electron microscopy. Most colacosome-forming species have been assigned to &lt;i&gt;Microbotryomycetes&lt;/i&gt; (&lt;i&gt;Pucciniomycotina&lt;/i&gt;, &lt;i&gt;Basidiomycota&lt;/i&gt;), a highly diverse class, comprising saprobic yeasts, mycoparasites, and phytoparasites. In general, these myco- and phytoparasites are dimorphic organisms, with a parasitic filamentous morph and saprobic yeast morph. We investigated colacosome-forming mycoparasites based on fungarium material, freshly collected specimens, and cultures of yeast morphs. We characterised the micromorphology of filamentous morphs, the physiological characteristics of yeast morphs, and inferred phylogenetic relationships based on DNA sequence data from seven loci. We outline and employ an epifluorescence-based microscopic method to assess the presence and organisation of colacosomes. We describe five new species in the genus &lt;i&gt;Colacogloea&lt;/i&gt;, the novel dimorphic mycoparasite &lt;i&gt;Mycogloiocolax gerardii&lt;/i&gt;, and provide the first report of a sexual, mycoparasitic morph in &lt;i&gt;Colacogloea philyla&lt;/i&gt; and in the genus &lt;i&gt;Slooffia&lt;/i&gt;. We detected colacosomes in eight fungal species, which brings the total number of known colacosome-forming fungi to 27. Finally, we revealed three distinct types of colacosome organisation in &lt;i&gt;Microbotryomycetes&lt;/i&gt;. &lt;b&gt;Taxonomic novelties and typifications:&lt;/b&gt; &lt;b&gt;New family:&lt;/b&gt; &lt;i&gt;Mycogloiocolacaeae&lt;/i&gt; Schoutteten & Yurkov; &lt;b&gt;New genus:&lt;/b&gt; &lt;i&gt;Mycogloiocolax&lt;/i&gt; Schoutteten & Rödel; &lt;b&gt;New species:&lt;/b&gt; &lt;i&gt;Colacogloea bettinae&lt;/i&gt; Schoutteten & Begerow, &lt;i&gt;C. biconidiata&lt;/i&gt; Schoutteten, &lt;i&gt;C. fennica&lt;/i&gt; Schoutteten & Miettinen, &lt;i&gt;C. microspora&lt;/i&gt; Schoutteten, &lt;i&gt;C. universitatis-gandavensis&lt;/i&gt; Schoutteten & Verbeken, &lt;i&gt;Mycogloiocolax gerardii&lt;/i&gt; Schoutteten & Rödel; &lt;b&gt;New combinations:&lt;/b&gt; &lt;i&gt;Slooffia micra&lt;/i&gt; (Bourdot & Galzin) Schoutteten, &lt;i&gt;Fellozyma cerberi&lt;/i&gt; (A.M. Yurkov &lt;i&gt;et al.&lt;/i&gt;) Schoutteten & Yurkov, &lt;i&gt;Fellozyma telluris&lt;/i&gt; (A.M. Yurkov &lt;i&gt;et al.&lt;/i&gt;) Schoutteten & Yurkov; &lt;b&gt;Epitypifications (basionyms):&lt;/b&gt; &lt;i&gt;Achroomyces insignis&lt;/i&gt; Hauerslev, &lt;i&gt;Platygloea micra&lt;/i&gt; Bourdot & Galzin, &lt;i&gt;Platygloea peniophorae&lt;/i&gt; Bourdot & Galzin; &lt;b&gt;Lectotypification (basionym):&lt;/b&gt; &lt;i&gt;Platygloea peniophorae&lt;/i&gt; Bourdot & Galzin &lt;b&gt;Citation:&lt;/b&gt; Schoutteten N, Yurkov A, Leroux O, Haelewaters D, Van Der Straeten D, Miettinen O, Boekhout T, Begerow D, Verbeken A (2023). Diversity of colacosome-interacting mycoparasites expands the understanding of the evolution and ecology of &lt;i&gt;Microbotryomycetes&lt;/i&gt;. &lt;i&gt;Studies in ","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"106 ","pages":"41-94"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In search of lost ergots: phylogenetic re-evaluation of <i>Claviceps</i> species in Japan and their biogeographic patterns revealed.","authors":"E Tanaka, K Tanada, T Hosoe, B Shrestha, M Kolařík, M Liu","doi":"10.3114/sim.2023.106.01","DOIUrl":"10.3114/sim.2023.106.01","url":null,"abstract":"<p><p><i>Claviceps</i> (<i>Clavicipitaceae</i>, <i>Hypocreales</i>) was erected in 1853, although ergotism had been well-known for a much longer time. By 2000, about 70 taxa had been described in <i>Claviceps</i>, of which eight species and six varieties were based on Japanese type or authentic specimens. Most of these Japanese <i>Claviceps</i> taxa are based on lost specimens or have invalid names, which means many species practically exist only in the scientific literature. The ambiguous identities of these species have hindered taxonomic resolution of the genus <i>Claviceps</i>. Consequently, we sought and collected more than 300 fresh specimens in search of the lost Japanese ergots. Multilocus phylogenetic analyses based on DNA sequences from LSU, <i>TEF-1α</i>, <i>TUB2</i>, <i>Mcm7</i>, and <i>RPB2</i> revealed the phylogenetic relationships between the Japanese specimens and known <i>Claviceps</i> spp., as well as the presence of biogeographic patterns. Based on the phylogenetic analysis, host range and morphology, we re-evaluated Japanese <i>Claviceps</i> and recognised at least 21 species in Japan. Here we characterised 14 previously described taxa and designated neo-, lecto- and epi-types for <i>C. bothriochloae</i>, <i>C. imperatae</i>, <i>C. litoralis, C. microspora</i>, <i>C. panicoidearum</i> and <i>C. yanagawaensis</i>. Two varieties were elevated to species rank with designated neotypes, <i>i.e.</i> <i>C. agropyri</i> and <i>C. kawatanii</i>. Six new species, <i>C. miscanthicola</i>, <i>C. oplismeni</i>, <i>C. palustris</i>, <i>C. phragmitis</i>, <i>C. sasae</i> and <i>C. tandae</i> were proposed and described. <b>Taxonomic novelties:</b> <b>New species:</b> <i>Claviceps miscanthicola</i> E. Tanaka, <i>Claviceps oplismeni</i> E. Tanaka, <i>Claviceps palustris</i> E. Tanaka, <i>Claviceps phragmitis</i> E. Tanaka, <i>Claviceps sasae</i> E. Tanaka, <i>Claviceps tandae</i> E. Tanaka; <b>New status and combination:</b> <i>Claviceps agropyri</i> (Tanda) E. Tanaka, <i>Claviceps kawatanii</i> (Tanda) E. Tanaka; <b>Typifications (basionyms):</b> <b>Lecto- and epitypification:</b> <i>Claviceps yanagawaensis</i> Togashi; <b>Neotypifications</b>: <i>Claviceps purpurea</i> var. <i>agropyri</i> Tanda, <i>Claviceps bothriochloae</i> Tanda & Y. Muray, <i>Claviceps imperatae</i> Tanda & Kawat., <i>Claviceps microspora</i> var. <i>kawatanii</i> Tanda, <i>Claviceps litoralis</i> Kawat., <i>Claviceps microspora</i> Tanda, <i>Claviceps panicoidearum</i> Tanda & Y. Harada; <b>Resurrection</b>: <i>Claviceps queenslandica</i> Langdon. <b>Citation</b>: Tanaka E, Tanada K, Hosoe T, Shrestha B, Kolařík M, Liu M (2023). In search of lost ergots: phylogenetic re-evaluation of <i>Claviceps</i> species in Japan and their biogeographic patterns revealed. <i>Studies in Mycology</i> <b>106</b>: 1-39. doi: 10.3114/sim.2022.106.01.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"106 ","pages":"1-39"},"PeriodicalIF":14.1,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10825747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Fusarium</i> diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus.","authors":"S L Han, M M Wang, Z Y Ma, M Raza, P Zhao, J M Liang, M Gao, Y J Li, J W Wang, D M Hu, L Cai","doi":"10.3114/sim.2022.104.02","DOIUrl":"10.3114/sim.2022.104.02","url":null,"abstract":"<p><p><i>Fusarium</i> species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of <i>Fusarium</i> diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 <i>Fusarium</i> strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated <i>Fusarium</i> species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one <i>Fusarium</i> species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the \"narrow\" generic concept of <i>Fusarium</i> (= <i>Gibberella</i>). This study represents one of the most comprehensive surveys of cereal <i>Fusarium</i> diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated <i>Fusarium</i> species, as well as largely clarifies the phylogenetic relationships within the genus. <b>Taxonomic novelties:</b> <b>New species:</b> <i>Fusarium erosum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium fecundum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium jinanense</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium mianyangense</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium nothincarnatum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium planum</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium sanyaense</i> S.L. Han, M.M. Wang & L. Cai, <i>Fusarium weifangense</i> S.L. Han, M.M. Wang & L. Cai. <b>Citation:</b> Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). <i>Fusarium</i> diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. <i>Studies in Mycology</i> <b>104</b>: 87-148. doi: 10.3114/sim.2022.104.02.</p>","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"104 ","pages":"87-148"},"PeriodicalIF":14.1,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10282163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9712358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lessons on fruiting body morphogenesis from genomes and transcriptomes of <i>Agaricomycetes</i>.","authors":"L G Nagy,&nbsp;P J Vonk,&nbsp;M Künzler,&nbsp;C Földi,&nbsp;M Virágh,&nbsp;R A Ohm,&nbsp;F Hennicke,&nbsp;B Bálint,&nbsp;Á Csernetics,&nbsp;B Hegedüs,&nbsp;Z Hou,&nbsp;X B Liu,&nbsp;S Nan,&nbsp;M Pareek,&nbsp;N Sahu,&nbsp;B Szathmári,&nbsp;T Varga,&nbsp;H Wu,&nbsp;X Yang,&nbsp;Z Merényi","doi":"10.3114/sim.2022.104.01","DOIUrl":"https://doi.org/10.3114/sim.2022.104.01","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (&lt;i&gt;Agaricomycetes&lt;/i&gt;) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of &lt;i&gt;Coprinopsis cinerea&lt;/i&gt;, and their orthologs in &lt;i&gt;Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus&lt;/i&gt;, and &lt;i&gt;Schizophyllum commune&lt;/i&gt;, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the &lt;i&gt;Agaricomycetes&lt;/i&gt;. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. &lt;b&gt;Citation:&lt;/b&gt; Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of &lt;i&gt;Agaricomycetes. Studies in Mycology&lt;/i&gt; &lt;b&gt;104&lt;/b&gt;: 1-85. doi: 10","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"104 ","pages":"1-85"},"PeriodicalIF":16.5,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10282164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9713175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome-informed higher rank classification of the biotechnologically important fungal subphylum <i>Saccharomycotina</i>.","authors":"M Groenewald, C T Hittinger, K Bensch, D A Opulente, X-X Shen, Y Li, C Liu, A L LaBella, X Zhou, S Limtong, S Jindamorakot, P Gonçalves, V Robert, K H Wolfe, C A Rosa, T Boekhout, N Čadež, G Éter, J P Sampaio, M-A Lachance, A M Yurkov, H-M Daniel, M Takashima, K Boundy-Mills, D Libkind, K Aoki, T Sugita, A Rokas","doi":"10.3114/sim.2023.105.01","DOIUrl":"10.3114/sim.2023.105.01","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The subphylum &lt;i&gt;Saccharomycotina&lt;/i&gt; is a lineage in the fungal phylum &lt;i&gt;Ascomycota&lt;/i&gt; that exhibits levels of genomic diversity similar to those of plants and animals. The &lt;i&gt;Saccharomycotina&lt;/i&gt; 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 &lt;i&gt;Saccharomycotina&lt;/i&gt; has much higher rates of genome sequence evolution than its sister subphylum, &lt;i&gt;Pezizomycotina&lt;/i&gt;, it contains only one class compared to the 16 classes in &lt;i&gt;Pezizomycotina&lt;/i&gt;. The third subphylum of &lt;i&gt;Ascomycota&lt;/i&gt;, the &lt;i&gt;Taphrinomycotina&lt;/i&gt;, consists of six classes and has approximately 10 times fewer species than the &lt;i&gt;Saccharomycotina&lt;/i&gt;. 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 &lt;i&gt;Saccharomycotina&lt;/i&gt; contains 12 major and robustly supported phylogenetic clades; seven of these are current families (&lt;i&gt;Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae&lt;/i&gt;, and &lt;i&gt;Saccharomycetaceae&lt;/i&gt;), one comprises two current families (&lt;i&gt;Dipodascaceae&lt;/i&gt; and &lt;i&gt;Trichomonascaceae&lt;/i&gt;), one represents the genus &lt;i&gt;Sporopachydermia&lt;/i&gt;, 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 &lt;i&gt;Saccharomycotina&lt;/i&gt;, 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 &lt;i&gt;Saccharomycotina&lt;/i&gt; more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. &lt;b&gt;Taxonomic novelties: New classes:&lt;/b&gt; &lt;i&gt;Alloascoideomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Dipodascomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Lipomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente, A. Rokas, &lt;i&gt;Pichiomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Sporopachydermiomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas, &lt;i&gt;Trigonopsidomycetes&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas. &lt;b&gt;New orders:&lt;/b&gt; &lt;i&gt;&lt;b&gt;Alloascoideomycetes:&lt;/b&gt;&lt;/i&gt; &lt;i&gt;Alloascoideales&lt;/i&gt; M. Groenew., Hittinger, Opulente & A. Rokas; &lt;i&gt;&lt;b&gt;Di","PeriodicalId":22036,"journal":{"name":"Studies in Mycology","volume":"1 1","pages":"1-22"},"PeriodicalIF":14.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11182611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69600543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}