Pub Date : 2025-06-01Epub Date: 2025-05-23DOI: 10.3114/persoonia.2025.54.08
M R Silva, F Paraíso, J Al-Oboudi, M Abegg, A Aires, K O Barros, P H Brito, M Jarzyna, K Sylvester, Q K Langdon, D A Opulente, F Carriconde, J W Fell, T A Hofmann, M-A Lachance, J-L Legras, D Libkind, A Pontes, P Gonçalves, C A Rosa, M Groenewald, C T Hittinger, J P Sampaio
The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species, T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains 10 species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how the complex relationship between key genes and the physiological traits they control both between and within species. This remarkable increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomic approaches can foster the assessment of species circumscriptions in fungi. Citation: Silva MR, Paraíso F, Al-Oboudi J, Abegg M, Aires A, Barros KO, Brito PH, Jarzyna M, Sylvester K, Langdon QK, Opulente DA, Carriconde F, Fell JW, Hofmann TA, Lachance M-A, Legras J-L, Libkind D, Pontes A, Gonçalves P, Rosa CA, Groenewald M, Hittinger CT, Sampaio JP (2025). A taxogenomic view of the genus Torulaspora: an expansion from ten to twenty-two species. Persoonia54: 265-283. doi: 10.3114/persoonia.2025.54.08.
Torulaspora酵母属（Saccharomycotina亚门，saccharomycaceae科）主要以其模式种T. delbrueckii而为人所知，T. delbrueckii是葡萄酒和酵母面包发酵的常客。该属目前包含10种，通常在温带和热带气候的各种自然陆生环境中发现。在这里，我们采用分类基因组学分析来调查我们在亚洲、澳大拉西亚、北美、南美和欧洲进行的多次调查中获得的大量Torulaspora菌株，并在培养收藏中添加了一些菌株。我们的分析发现了这里正式描述的12个新物种，从而使Torulaspora的物种多样性增加了一倍以上。我们还绘制了该属的基因型-表型图谱，并展示了关键基因与它们在物种之间和物种内控制的生理性状之间的复杂关系。Torulaspora属物种数量的显著增加突出了真菌分类群目前的库存是多么有限。它还显示了整合的分类基因组方法如何促进真菌物种界限的评估。引用本文：Silva MR， Paraíso F, Al-Oboudi J, Abegg M, Aires A, Barros KO, Brito PH, Jarzyna M, Sylvester K, Langdon QK, Opulente DA, Carriconde F, Fell JW, Hofmann TA, Lachance M-A, Legras J- l, Libkind D, Pontes A, gonalves P, Rosa CA, Groenewald M, Hittinger CT, Sampaio JP（2025）。虎蛛属的分类基因组学观点：从10种扩展到22种。《人》54:265-283。doi: 10.3114 / persoonia.2025.54.08。
{"title":"A taxogenomic view of the genus <i>Torulaspora</i>: an expansion from ten to twenty-two species.","authors":"M R Silva, F Paraíso, J Al-Oboudi, M Abegg, A Aires, K O Barros, P H Brito, M Jarzyna, K Sylvester, Q K Langdon, D A Opulente, F Carriconde, J W Fell, T A Hofmann, M-A Lachance, J-L Legras, D Libkind, A Pontes, P Gonçalves, C A Rosa, M Groenewald, C T Hittinger, J P Sampaio","doi":"10.3114/persoonia.2025.54.08","DOIUrl":"10.3114/persoonia.2025.54.08","url":null,"abstract":"<p><p>The yeast genus <i>Torulaspora</i> (subphylum <i>Saccharomycotina</i>, family <i>Saccharomycetaceae</i>) is mostly known from its type species, <i>T. delbrueckii</i>, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains 10 species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of <i>Torulaspora</i> strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of <i>Torulaspora</i>. We also sketch a genotype-phenotype map for the genus and show how the complex relationship between key genes and the physiological traits they control both between and within species. This remarkable increase in the number of species in the genus <i>Torulaspora</i> highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomic approaches can foster the assessment of species circumscriptions in fungi. <b>Citation:</b> Silva MR, Paraíso F, Al-Oboudi J, Abegg M, Aires A, Barros KO, Brito PH, Jarzyna M, Sylvester K, Langdon QK, Opulente DA, Carriconde F, Fell JW, Hofmann TA, Lachance M-A, Legras J-L, Libkind D, Pontes A, Gonçalves P, Rosa CA, Groenewald M, Hittinger CT, Sampaio JP (2025). A taxogenomic view of the genus <i>Torulaspora</i>: an expansion from ten to twenty-two species. <i>Persoonia</i> <b>54</b>: 265-283. doi: 10.3114/persoonia.2025.54.08.</p>","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"54 ","pages":"265-283"},"PeriodicalIF":7.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12308288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760719","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}
Pub Date : 2025-06-01Epub Date: 2025-07-08DOI: 10.3114/persoonia.2025.54.10
P W Crous, D E A Catcheside, P S Catcheside, A C Alfenas, R F Alfenas, R W Barreto, T Lebel, S Balashov, J Broadbridge, Ž Jurjević, S De la Peña-Lastra, R Hoffmann, A Mateos, J Riebesehl, R G Shivas, F F Soliz Santander, Y P Tan, A Altés, D Bandini, F Carriconde, J Cazabonne, P Czachura, H Gryta, G Eyssartier, E Larsson, O L Pereira, A Rigueiro-Rodríguez, M J Wingfield, W Ahmad, S Bibi, S Denman, F Esteve-Raventós, S Hussain, T Illescas, J J Luangsa-Ard, L Möller, A Mombert, W Noisripoom, I Olariaga, F Pancorbo, A Paz, M Piątek, C Polman-Short, E Suárez, N S Afshan, H Ali, M Arzanlou, F Ayer, J Barratt, J-M Bellanger, A Bidaud, S L Bishop-Hurley, M Bohm, T Bose, E Campo, N B Chau, Ö F Çolak, T R L Cordeiro, M O Cruz, F A Custódio, A Couceiro, V Darmostuk, J D W Dearnaley, A L C M de Azevedo Santiago, L W S de Freitas, M de J Yáñez-Morales, C Domnauer, B Dentinger, K Dhileepan, J T De Souza, F Dovana, U Eberhardt, P Eisvand, A Erhard, V Fachada, A García-Martín, M Groenewald, A Hammerbacher, K Harms, S Haroon, M Haqnawaz, S Henriques, A J Hernández, L M Jacobus, D Jaen-Contreras, P Jangsantear, O Kaygusuz, R Knoppersen, T K A Kumar, M J Lynch, R Mahiques, G L Maraia, P A S Marbach, M Mehrabi-Koushki, P R Miller, S Mongkolsamrit, P-A Moreau, N H Oberlies, J A Oliveira, D Orlovich, A S Pérez-Méndez, A Pinto, H A Raja, G H Ramírez, B Raphael, A Rodrigues, H Rodrigues, D O Ramos, A Safi, S Sarwar, I Saar, R M Sánchez, J S Santana, J Scrace, L S Sales, L N P Silva, M Stryjak-Bogacka, A Tacconi, V N Thanh, A Thomas, N T Thuy, M Toome, J M Valdez-Carrazco, N I van Vuuren, J Vasey, J Vauras, C Vila-Viçosa, M Villarreal, C M Visagie, A Vizzini, E J Whiteside, J Z Groenewald
Novel species of fungi described in this study include those from various countries as follows: Argentina, Septoria reinamora on leaf spots of Mutisia spinosa. Australia, Cortinarius albofolliculus on mossy soil, Cortinarius descensoriformis among leaf litter, Cortinarius kaki among leaf litter, Cortinarius lissosporus in leaf litter, Cortinarius malogranatus in leaf litter, Cortinarius meletlac on soil in mixed forest, Cortinarius sebosioides in long decayed wood litter, Helicogermslita australiensis as an endophyte from healthy leaves of Archontophoenix cunninghamiana, Puccinia clemensiorum on culms of Eleocharis ochrostachys, Puccinia geethae on leaves of Cyperus brevifolius, Puccinia marjaniae on leaves of Nymphoides indica, Puccinia scleriae-rugosae on leaves of Scleria rugosa. Brazil, Dactylaria calliandrae on living leaf of Calliandra tweediei, Mucor cerradoensis from soil, Musicillium palmae on living leaves of unidentified palm species, Neodendryphiella agapanthi from stalks of Agapanthus praecox, Parafusicladium riodejaneiroanum on living leaves of native bamboo, Parapenidiella melastomatis on living leaves of unidentified Melastomataceae, Pararamichloridium ouropretoense on living leaves of unidentified Poaceae, Pentagonomyces endophyticus (incl. Pentagonomyces gen. nov.) as endophytic from roots of Musa acuminata, Polyschema endophytica from healthy roots of coffee plant, Purimyces endophyticus as root endophyte of Cattleya locatellii, Ramularia rhododendri on living leaves of Rhododendron sp., Staphylotrichum soli from soil, Trichoderma sexdentis from leaves inside a nest of the leaf-cutting ant Atta sexdens rubropilosa, Wiesneriomyces soli from soil. France, Cosmospora nemaniae on dead or effete stromata of Nemania cf. colliculosa, Inocybe alnobetulae in subalpine green alder stands, Stylonectria hygrophila on dead twigs of Betula pubescens.Germany, Coniochaeta corticalis from bark humus, Coniochaeta fermentaria from fermentation residues from biogas plants, Coniochaeta fibricola from softwood fibres, Coniochaeta weberae from bark humus, Inocybe canicularis on calcareous to more acidic soil with conifers. Iceland, Inocybe islandica associated with Dryas octopetala. India, Vishniacozyma indica on dead twigs. Iran, Botryotrichum lycii on rotten leaf of Lycium depressum.Italy, Cuphophyllus dolomiticus among Salix retusa, Salix reticulata and Dryas octopetala, Inocybe subentolomospora on moss with the presence of Alnus incana, Populus nigra and
{"title":"Fungal Planet description sheets: 1781-1866.","authors":"P W Crous, D E A Catcheside, P S Catcheside, A C Alfenas, R F Alfenas, R W Barreto, T Lebel, S Balashov, J Broadbridge, Ž Jurjević, S De la Peña-Lastra, R Hoffmann, A Mateos, J Riebesehl, R G Shivas, F F Soliz Santander, Y P Tan, A Altés, D Bandini, F Carriconde, J Cazabonne, P Czachura, H Gryta, G Eyssartier, E Larsson, O L Pereira, A Rigueiro-Rodríguez, M J Wingfield, W Ahmad, S Bibi, S Denman, F Esteve-Raventós, S Hussain, T Illescas, J J Luangsa-Ard, L Möller, A Mombert, W Noisripoom, I Olariaga, F Pancorbo, A Paz, M Piątek, C Polman-Short, E Suárez, N S Afshan, H Ali, M Arzanlou, F Ayer, J Barratt, J-M Bellanger, A Bidaud, S L Bishop-Hurley, M Bohm, T Bose, E Campo, N B Chau, Ö F Çolak, T R L Cordeiro, M O Cruz, F A Custódio, A Couceiro, V Darmostuk, J D W Dearnaley, A L C M de Azevedo Santiago, L W S de Freitas, M de J Yáñez-Morales, C Domnauer, B Dentinger, K Dhileepan, J T De Souza, F Dovana, U Eberhardt, P Eisvand, A Erhard, V Fachada, A García-Martín, M Groenewald, A Hammerbacher, K Harms, S Haroon, M Haqnawaz, S Henriques, A J Hernández, L M Jacobus, D Jaen-Contreras, P Jangsantear, O Kaygusuz, R Knoppersen, T K A Kumar, M J Lynch, R Mahiques, G L Maraia, P A S Marbach, M Mehrabi-Koushki, P R Miller, S Mongkolsamrit, P-A Moreau, N H Oberlies, J A Oliveira, D Orlovich, A S Pérez-Méndez, A Pinto, H A Raja, G H Ramírez, B Raphael, A Rodrigues, H Rodrigues, D O Ramos, A Safi, S Sarwar, I Saar, R M Sánchez, J S Santana, J Scrace, L S Sales, L N P Silva, M Stryjak-Bogacka, A Tacconi, V N Thanh, A Thomas, N T Thuy, M Toome, J M Valdez-Carrazco, N I van Vuuren, J Vasey, J Vauras, C Vila-Viçosa, M Villarreal, C M Visagie, A Vizzini, E J Whiteside, J Z Groenewald","doi":"10.3114/persoonia.2025.54.10","DOIUrl":"10.3114/persoonia.2025.54.10","url":null,"abstract":"<p><p>Novel species of fungi described in this study include those from various countries as follows: <b>Argentina</b>, <i>Septoria reinamora</i> on leaf spots of <i>Mutisia spinosa</i>. <b>Australia</b>, <i>Cortinarius albofolliculus</i> on mossy soil, <i>Cortinarius descensoriformis</i> among leaf litter, <i>Cortinarius kaki</i> among leaf litter, <i>Cortinarius lissosporus</i> in leaf litter, <i>Cortinarius malogranatus</i> in leaf litter, <i>Cortinarius meletlac</i> on soil in mixed forest, <i>Cortinarius sebosioides</i> in long decayed wood litter, <i>Helicogermslita australiensis</i> as an endophyte from healthy leaves of <i>Archontophoenix cunninghamiana</i>, <i>Puccinia clemensiorum</i> on culms of <i>Eleocharis ochrostachys, Puccinia geethae</i> on leaves of <i>Cyperus brevifolius</i>, <i>Puccinia marjaniae</i> on leaves of <i>Nymphoides indica, Puccinia scleriae-rugosae</i> on leaves of <i>Scleria rugosa</i>. <b>Brazil</b>, <i>Dactylaria calliandrae</i> on living leaf of <i>Calliandra tweediei, Mucor cerradoensis</i> from soil, <i>Musicillium palmae</i> on living leaves of unidentified palm species, <i>Neodendryphiella agapanthi</i> from stalks of <i>Agapanthus praecox</i>, <i>Parafusicladium riodejaneiroanum</i> on living leaves of native bamboo, <i>Parapenidiella melastomatis</i> on living leaves of unidentified <i>Melastomataceae</i>, <i>Pararamichloridium ouropretoense</i> on living leaves of unidentified <i>Poaceae</i>, <i>Pentagonomyces endophyticus</i> (incl. <i>Pentagonomyces gen. nov.</i>) as endophytic from roots of <i>Musa acuminata</i>, <i>Polyschema endophytica</i> from healthy roots of coffee plant, <i>Purimyces endophyticus</i> as root endophyte of <i>Cattleya locatellii, Ramularia rhododendri</i> on living leaves of <i>Rhododendron</i> sp., <i>Staphylotrichum soli</i> from soil, <i>Trichoderma sexdentis</i> from leaves inside a nest of the leaf-cutting ant <i>Atta sexdens rubropilosa</i>, <i>Wiesneriomyces soli</i> from soil. <b>France</b>, <i>Cosmospora nemaniae</i> on dead or effete stromata of <i>Nemania</i> cf. <i>colliculosa</i>, <i>Inocybe alnobetulae</i> in subalpine green alder stands, <i>Stylonectria hygrophila</i> on dead twigs of <i>Betula pubescens.</i> <b>Germany</b>, <i>Coniochaeta corticalis</i> from bark humus, <i>Coniochaeta fermentaria</i> from fermentation residues from biogas plants, <i>Coniochaeta fibricola</i> from softwood fibres, <i>Coniochaeta weberae</i> from bark humus, <i>Inocybe canicularis</i> on calcareous to more acidic soil with conifers. <b>Iceland</b>, <i>Inocybe islandica</i> associated with <i>Dryas octopetala</i>. <b>India</b>, <i>Vishniacozyma indica</i> on dead twigs. <b>Iran</b>, <i>Botryotrichum lycii</i> on rotten leaf of <i>Lycium depressum.</i> <b>Italy</b>, <i>Cuphophyllus dolomiticus</i> among <i>Salix retusa</i>, <i>Salix reticulata</i> and <i>Dryas octopetala</i>, <i>Inocybe subentolomospora</i> on moss with the presence of <i>Alnus incana</i>, <i>Populus nigra</i> and <i>","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"54 ","pages":"327-587"},"PeriodicalIF":7.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12308287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760787","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}
Pub Date : 2025-06-01Epub Date: 2025-05-14DOI: 10.3114/persoonia.2025.54.06
K Zhang, M Sandoval-Denis, H Kandemir, N Yilmaz, J Z Groenewald, F Roets, M de J Yáñez-Morales, M J Wingfield, P W Crous
Species of Bisifusarium (previously the Fusarium dimerum species complex) have been associated with cheese fermentation and a wide range of opportunistic human infections, but they are generally regarded as saprotrophs. Bisifusarium spp. are also commonly isolated from soils and tissues of plants growing in arid climates. The genus is typically characterized by its distinct pionnotal growth in culture, and typically very short, 0-2(-3)-septate macroconidia, produced in sporodochia or on lateral phialidic hyphal pegs. Only 16 species of Bisifusarium have been described to date, and this study sought to re-evaluate these taxa by examining 116 Bisifusarium isolates from the culture collection of the Westerdijk Fungal Biodiversity Institute in Utrecht, The Netherlands. A multi-gene phylogenetic analysis using partial nucleotide sequences of the translation elongation factor 1-alpha (tef1), partial RNA polymerase II second largest subunit (rpb2), the 5.8S nrDNA with its flanking intergenic spacer regions (ITS), and partial β-tubulin (tub2) genes resolved 25 phylogenetic lineages. Further evaluation of culture and morphological characters, and host-substrates, confirmed eight of these clades as novel taxa that are formally described here. In addition, two putative novel species were identified but not described due to limited available data. We provide the morphological descriptions and photographic illustrations for B. hedylamarriae and B. lovelliae, which were formerly known only from their DNA data. This study significantly increases the number of species in Bisifusarium and provides a crucial foundation for future studies to elucidate the ecology and evolutionary relationships within this expanding genus. Citation: Zhang K, Sandoval-Denis M, Kandemir H, Yilmaz N, Groenewald JZ, Roets F, Yáñez-Morales M de J, Wingfield MJ, Crous PW (2025). Taxonomic revision of Bifusarium (Nectriaceae). Persoonia54: 197-223. doi: 10.3114/persoonia.2025.54.06.
双歧镰刀菌（以前称为二角镰刀菌）与奶酪发酵和广泛的机会性人类感染有关，但它们通常被认为是腐生菌。双镰刀菌通常也从生长在干旱气候的植物的土壤和组织中分离出来。该属的典型特征是其在培养中具有明显的先头生长，并且通常非常短，0-2（-3）分隔的大分生孢子，产生于孢子体或侧边的亲性菌丝柱上。迄今为止，只有16种Bisifusarium被描述，本研究试图通过检查荷兰乌得勒支Westerdijk真菌生物多样性研究所培养的116株Bisifusarium分离株来重新评估这些分类群。利用翻译延伸因子1- α (tef1)、部分RNA聚合酶II第二大亚基（rpb2）、5.8S nrDNA及其侧翼基因间间隔区（its）和部分β-微管蛋白（tub2）基因的部分核苷酸序列进行多基因系统发育分析，确定了25个系统发育谱系。对培养和形态特征以及宿主-基质的进一步评估证实，其中8个分支是本文正式描述的新分类群。此外，还发现了两个假定的新种，但由于现有资料有限，没有对其进行描述。我们提供了B. hedylamarriae和B. lovelliae的形态描述和照片插图，这两种植物以前只从它们的DNA数据中得知。该研究显著增加了双菜属植物的种类数量，为进一步研究这一不断扩大的属的生态学和进化关系奠定了重要基础。引用本文：张科，Sandoval-Denis M, Kandemir H, Yilmaz N, Groenewald JZ, Roets F, Yáñez-Morales M de J, Wingfield MJ, Crous PW（2025）。标题双歧花属植物的分类订正。《人物》54:197-223。doi: 10.3114 / persoonia.2025.54.06。
{"title":"Taxonomic revision of <i>Bisifusarium</i> (<i>Nectriaceae</i>).","authors":"K Zhang, M Sandoval-Denis, H Kandemir, N Yilmaz, J Z Groenewald, F Roets, M de J Yáñez-Morales, M J Wingfield, P W Crous","doi":"10.3114/persoonia.2025.54.06","DOIUrl":"10.3114/persoonia.2025.54.06","url":null,"abstract":"<p><p>Species of <i>Bisifusarium</i> (previously the <i>Fusarium dimerum</i> species complex) have been associated with cheese fermentation and a wide range of opportunistic human infections, but they are generally regarded as saprotrophs. <i>Bisifusarium</i> spp. are also commonly isolated from soils and tissues of plants growing in arid climates. The genus is typically characterized by its distinct pionnotal growth in culture, and typically very short, 0-2(-3)-septate macroconidia, produced in sporodochia or on lateral phialidic hyphal pegs. Only 16 species of <i>Bisifusarium</i> have been described to date, and this study sought to re-evaluate these taxa by examining 116 <i>Bisifusarium</i> isolates from the culture collection of the Westerdijk Fungal Biodiversity Institute in Utrecht, The Netherlands. A multi-gene phylogenetic analysis using partial nucleotide sequences of the translation elongation factor 1-alpha (<i>tef1</i>), partial RNA polymerase II second largest subunit (<i>rpb2</i>), the 5.8S nrDNA with its flanking intergenic spacer regions (ITS), and partial β-tubulin (<i>tub2</i>) genes resolved 25 phylogenetic lineages. Further evaluation of culture and morphological characters, and host-substrates, confirmed eight of these clades as novel taxa that are formally described here. In addition, two putative novel species were identified but not described due to limited available data. We provide the morphological descriptions and photographic illustrations for <i>B. hedylamarriae</i> and <i>B. lovelliae</i>, which were formerly known only from their DNA data. This study significantly increases the number of species in <i>Bisifusarium</i> and provides a crucial foundation for future studies to elucidate the ecology and evolutionary relationships within this expanding genus. <b>Citation:</b> Zhang K, Sandoval-Denis M, Kandemir H, Yilmaz N, Groenewald JZ, Roets F, Yáñez-Morales M de J, Wingfield MJ, Crous PW (2025). Taxonomic revision of <i>Bifusarium</i> (<i>Nectriaceae</i>). <i>Persoonia</i> <b>54</b>: 197-223. doi: 10.3114/persoonia.2025.54.06.</p>","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"54 ","pages":"197-223"},"PeriodicalIF":7.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12308283/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760790","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}
The genera Cephalotrichum and Microascus contain ecologically, morphologically and lifestyle diverse fungi in Microascaceae (Microascales, Sordariomycetes) with a world-wide distribution. Despite previous studies having elucidated that Cephalotrichum and Microascus are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most comprehensive multi-gene (ITS, LSU, tef1 and tub2) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of Microascaceae. Two previously recognised main clades, Cephalotrichum (24 species)and Microascus (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within Microascaceae. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to Cephalotrichum and Microascus, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of Microascaceae was around 210.37 Mya (95% HPD: 177.18–246.96 Mya) in the Late Triassic, and that Cephalotrichum and Microascus began to diversify approximately 27.07 Mya (95% HPD:20.47–34.37 Mya) and 70.46 Mya (95% HPD:56.96–86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help elucidate previously unresolved clade relationships.
{"title":"A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history","authors":"T.P. Wei, Y.M. Wu, X. Zhang, H. Zhang, P.W. Crous, Y.L. Jiang","doi":"10.3767/persoonia.2024.52.05","DOIUrl":"https://doi.org/10.3767/persoonia.2024.52.05","url":null,"abstract":"The genera<i> Cephalotrichum</i> and<i> Microascus</i> contain ecologically, morphologically and lifestyle diverse fungi in<i> Microascaceae</i> (<i>Microascales</i>,<i> Sordariomycetes</i>) with a world-wide distribution. Despite previous studies having elucidated that<i> Cephalotrichum</i>\u0000and<i> Microascus</i> are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most\u0000comprehensive multi-gene (ITS, LSU,<i> tef1</i> and<i> tub2</i>) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of<i> Microascaceae</i>. Two previously recognised main clades,<i> Cephalotrichum</i> (24 species)and<i> Microascus</i> (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within<i> Microascaceae</i>. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to<i> Cephalotrichum</i> and<i> Microascus</i>, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of<i> Microascaceae</i> was around 210.37 Mya (95% HPD: 177.18–246.96 Mya) in the Late Triassic,\u0000and that<i> Cephalotrichum</i> and<i> Microascus</i> began to diversify approximately 27.07 Mya (95% HPD:20.47–34.37 Mya) and 70.46 Mya (95% HPD:56.96–86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help\u0000elucidate previously unresolved clade relationships.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"22 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-30DOI: 10.3767/persoonia.2024.52.01
F. Liu, Z.-D. Hu, A. Yurkov, X.-H. Chen, W.-J. Bao, Q. Ma, W.-N. Zhao, S. Pan, X.-M. Zhao, J.-H. Liu, Q.-M. Wang, T. Boekhout
A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence- absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania , Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80–92% POCP values and a range of 60–70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations.
{"title":"Saccharomycetaceae: delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies","authors":"F. Liu, Z.-D. Hu, A. Yurkov, X.-H. Chen, W.-J. Bao, Q. Ma, W.-N. Zhao, S. Pan, X.-M. Zhao, J.-H. Liu, Q.-M. Wang, T. Boekhout","doi":"10.3767/persoonia.2024.52.01","DOIUrl":"https://doi.org/10.3767/persoonia.2024.52.01","url":null,"abstract":"A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses.\u0000However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters\u0000to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the\u0000presence- absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in<i> Saccharomycetaceae</i>, namely<i> Eremothecium</i>,<i> Grigorovia</i>,<i> Kazachstania</i>,<i> Kluyveromyces</i>,<i> Lachancea</i>,<i> Nakaseomyces</i>,<i> Naumovozyma</i>,<i> Saccharomyces</i>,<i> Tetrapisispora</i>,<i> Torulaspora</i>,<i> Vanderwaltozyma</i>,<i> Zygosaccharomyces</i> and<i> Zygotorulaspora. </i> As a result, most of these genera are supported by the genomics-based metrics, but the genera<i> Kazachstania</i> ,<i> Nakaseomyces </i> and<i> Tetrapisispora</i> were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80–92% POCP values and a range of 60–70 % AAI values\u0000might be valuable thresholds to discriminate genera in<i> Saccharomycetaceae.</i> Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in<i> Saccharomycetaceae</i>. Our results indicate\u0000that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera<i> Kazachstania</i>,<i> Nakaseomyces</i> and<i> Tetrapisispora</i>\u0000are revised and we propose eight new genera and 41 new combinations.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"12 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-30DOI: 10.3767/persoonia.2024.52.04
M. Mu, Y.-J. Choi, J. Kruse, J.A. Crouch, S. Ploch, M. Thines
The genus Peronospora is the largest genus of the oomycetes, fungus-like members of the kingdom Straminipila that also contains amoeboid (e.g., Leukarachnion) and plant-like (e.g., Laminaria) life forms. Peronospora species are obligate biotrophic plant pathogens, causing high economic losses in various crops and ornamentals, including Plantago species. Several species of Plantago are used as specialty crops and medicinal plants. In this study, Peronospora species parasitic on Plantago were investigated based on morphology and phylogenetic analyses using two nuclear (ITS, nrLSU) loci and one mitochondrial (cox2) locus. As a result of these investigations, 10 new species are added to the already known Peronospora species on Plantago. Interestingly, it was found that four independent species are parasitic to Plantago major, highlighting that the reliance on the host plant for pathogen determination can be misleading in Peronospora. Taking this into account, morphological and phylogenetic analyses should be conducted as a prerequisite for effective quarantine regulations and phytosanitary measures.
{"title":"Single host plant species may harbour more than one species of Peronospora – a case study on Peronospora infecting Plantag","authors":"M. Mu, Y.-J. Choi, J. Kruse, J.A. Crouch, S. Ploch, M. Thines","doi":"10.3767/persoonia.2024.52.04","DOIUrl":"https://doi.org/10.3767/persoonia.2024.52.04","url":null,"abstract":"The genus <i>Peronospora</i> is the largest genus of the oomycetes, fungus-like members of the kingdom <i>Straminipila</i> that also contains amoeboid (e.g., <i>Leukarachnion</i>) and plant-like (e.g., <i>Laminaria</i>) life forms. <i>Peronospora</i> species are obligate biotrophic\u0000plant pathogens, causing high economic losses in various crops and ornamentals, including <i>Plantago</i> species. Several species of <i>Plantago</i> are used as specialty crops and medicinal plants. In this study, <i>Peronospora</i> species parasitic on <i>Plantago</i> were investigated based\u0000on morphology and phylogenetic analyses using two nuclear (ITS, nrLSU) loci and one mitochondrial (cox2) locus. As a result of these investigations, 10 new species are added to the already known <i>Peronospora</i> species on <i>Plantago</i>. Interestingly, it was found that four independent\u0000species are parasitic to <i>Plantago majo</i>r, highlighting that the reliance on the host plant for pathogen determination can be misleading in <i>Peronospora</i>. Taking this into account, morphological and phylogenetic analyses should be conducted as a prerequisite for effective quarantine\u0000regulations and phytosanitary measures.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"2018 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-30DOI: 10.3767/persoonia.2024.52.02
F. Liu, Z.-D. Hu, X.-M. Zhao, W.-N. Zhao, Z.-X. Feng, A. Yurkov, S. Alwasel, T. Boekhout, K. Bensch, F.-L. Hui, F.-Y. Bai, Q.-M. Wang
Candida is a polyphyletic genus of sexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris - Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP), and the presence-absence patterns of orthologs (PAPO).Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced, and this will reduce the polyphyly of the genus Candida.
{"title":"Phylogenomic analysis of the Candida auris- Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species","authors":"F. Liu, Z.-D. Hu, X.-M. Zhao, W.-N. Zhao, Z.-X. Feng, A. Yurkov, S. Alwasel, T. Boekhout, K. Bensch, F.-L. Hui, F.-Y. Bai, Q.-M. Wang","doi":"10.3767/persoonia.2024.52.02","DOIUrl":"https://doi.org/10.3767/persoonia.2024.52.02","url":null,"abstract":"<i>Candida</i> is a polyphyletic genus of sexually reproducing yeasts in the <i>Saccharomycotina</i> with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades,\u0000approximately half of the <i>Candida</i> species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. <i>Candida auris</i> is an important, globally emerging opportunistic pathogen that has\u0000caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the <i>Candida auris</i> - <i>Candida haemuli</i> (CAH) clade in the <i>Metschnikowiaceae</i>, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from\u0000natural environments. The clade is phylogenetically positioned remotely from the type species of the genus <i>Candida</i> that is <i>Candida vulgaris</i> (currently interpreted as a synonym of <i>Candida tropicalis</i>) and belongs to the family <i>Debaryomycetaceae</i>. Although previous\u0000phylogenetic and phylogenomic studies confirmed the position of <i>C. auris</i> in the <i>Metschnikowiaceae</i>, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera <i>Clavispora</i> and <i>Metschnikowia</i>. To resolve the\u0000position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of <i>C. auris</i> and related species in the <i>Metschnikowiaceae</i> using several metrics, such as the average amino acid identity (AAI) values, the percentage\u0000of conserved proteins (POCP), and the presence-absence patterns of orthologs (PAPO).Based on those approaches, 13 new genera are proposed for various <i>Candida</i> and <i>Hyphopichia</i> species, including members of the CAH clade in the <i>Metschnikowiaceae</i>. As a result, <i>C. auris</i>\u0000and related species are reassigned to the genus <i>Candidozyma</i>. Fifty-five new combinations and nine new species are introduced, and this will reduce the polyphyly of the genus <i>Candida</i>.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"102 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-30DOI: 10.3767/persoonia.2024.52.03
M. Blázquez, I. Pérez-Vargas, I. Garrido-Benavent, M. Villar-dePablo, Y. Turégano, C. Frías-López, A. Sánchez-Gracia, A. de los Ríos, F. Gasulla, S. Pérez-Ortega
Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation.Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary, and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages.In order to use the Ramalina decipiens group as a model system, it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study, we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed, and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry, and geographic origin).We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics, and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi.
{"title":"Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group","authors":"M. Blázquez, I. Pérez-Vargas, I. Garrido-Benavent, M. Villar-dePablo, Y. Turégano, C. Frías-López, A. Sánchez-Gracia, A. de los Ríos, F. Gasulla, S. Pérez-Ortega","doi":"10.3767/persoonia.2024.52.03","DOIUrl":"https://doi.org/10.3767/persoonia.2024.52.03","url":null,"abstract":"Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in\u0000the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification\u0000patterns congruent with radiation.Here we propose the <i>Ramalina decipiens</i> group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens,\u0000Canary, and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages.In order to use the <i>Ramalina\u0000decipiens</i> group as a model system, it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study, we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are\u0000newly developed, and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry, and geographic origin).We found\u0000that taxonomic diversity in the <i>Ramalina decipiens</i> group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics, and provide a key to the group. Phylogenetic relationships among species have been reconstructed\u0000with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"17 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141585900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-31DOI: 10.3767/persoonia.2023.51.06
X.E. Xiao, Y.D. Liu, F. Zheng, T. Xiong, Y.T. Zeng, W. Wang, X.L. Zheng, Q. Wu, J.P. Xu, P.W. Crous, C. Jiao, H.Y. Li
Species in Diaporthe have broad host ranges and cosmopolitan geographic distributions, occurring as endophytes, saprobes and plantpathogens. Previous studies have indicated that many Diaporthe species are associated with Citrus. To further determine the diversity of Diaporthe species associated with citrus diseases in China, we conducted extensive surveys in major citrus-producing are as from 2017–2020. Diseased tissues we recollected from leaves, fruits, twigs, branches and trunks showing a range of symptoms including melanose, dieback, gummosis, wood decay and canker. Based on phylogenetic comparisons of DNA sequences of the internal transcribed spacer regions(ITS), calmodulin(cal), histoneH3(his3), translation elongation factor1-alpha (tef1) and beta-tubulin (tub2), 393 isolates from 10 provinces were identified as belonging to 36 species of Diaporthe, including 32 known species, namely D. apiculata, D. biconispora, D. biguttulata, D. caryae, D. citri, D. citriasiana, D. compacta, D. discoidispora, D. endophytica, D. eres, D. fusicola, D. fulvicolor, D. guangxiensis, D. hongkongensis, D. hubeiensis, D. limonicola, D. litchii, D. novem, D. passifloricola, D. penetriteum, D. pescicola, D. pometiae, D. sackstonii, D. sennicola, D. sojae, D. spinosa, D. subclavata, D. tectonae, D. tibetensis, D. unshiuensis, D. velutina and D. xishuangbanica, and four new species, namely D. gammata , D. jishouensis, D. ruiliensis and D. sexualispora. Among the 32 known species, 14 are reported for the first time on Citrus, and two are newly reported from China. Among the 36 species, D. citri was the dominant species as exemplified by its high frequency of isolationand virulence. Pathogenicity tests indicated that most Diaporthe species obtained in this study were weakly aggressive or non-pathogenic to the tested citrus varieties. Only D. citri produced the longest lesion lengths on citrus shoots and induced melanose on citrus leaves. These results further demonstrated that a rich diversity of Diaporthe species occupy Citrus, but only a few species are harmful and D. citri is the main pathogen for Citrus in China. The present study provides a basis from which targeted monitoring, prevention and control measures can be developed.
Diaporthe 物种的寄主范围很广，分布于世界各地，以内生菌、汁菌和植物病原体的形式出现。以前的研究表明，许多 Diaporthe 物种与柑橘相关。为进一步确定中国柑橘病害相关 Diaporthe 物种的多样性，我们于 2017-2020 年在柑橘主产区进行了广泛调查。我们从叶片、果实、树枝、枝条和树干中采集了病组织，这些病组织表现出一系列症状，包括黑斑病、枯死病、胶冻病、木质部腐烂病和腐烂病。根据内部转录间隔区（ITS）、钙调蛋白（cal）、组蛋白H3（his3）、翻译伸长因子1-α（tef1）和β-微管蛋白（tub2）的DNA序列的系统发育比较，从10个省的393个分离物中鉴定出属于36个Diaporthe种，包括32个已知种，即D.apiculata、D. biconispora、D. biguttulata、D. caryae、D. citri、D. citriasiana、D. compacta、D. discoidispora、D.endophytica, D. eres, D. fusicola, D. fulvicolor, D. guangxiensis, D. hongkongensis, D. hubeiensis, D. limonicola, D. litchii, D. novem, D. passifloricola, D. penetriteum, D. pescicola, D. pometiae, D. sackstonii, D. sennicola, D. so.sennicola、D. sojae、D. spinosa、D. subclavata、D. tectonae、D. tibetensis、D. unshiuensis、D. velutina 和 D. xishuangbanica，以及 4 个新种，即 D. gammata、D. jishouensis、D. ruiliensis 和 D. sexualispora。在 32 个已知种中，14 个是首次在柑橘上报道，2 个是中国新报道。在这 36 个种中，柑橘褐斑病菌是优势种，这体现在它的高分离频率和高致病力上。致病性测试表明，本研究中获得的大多数 Diaporthe 物种对受测柑橘品种的侵染性较弱或无致病性。只有 D. citri 在柑橘嫩枝上产生的病斑长度最长，并在柑橘叶片上诱发黑色素。这些结果进一步表明，柑橘上的 Diaporthe 种类丰富多样，但只有少数几个种类是有害的，而 D. citri 是中国柑橘的主要病原菌。本研究为制定有针对性的监测、预防和控制措施提供了依据。
{"title":"High species diversity in Diaporthe associated with citrus diseases in China","authors":"X.E. Xiao, Y.D. Liu, F. Zheng, T. Xiong, Y.T. Zeng, W. Wang, X.L. Zheng, Q. Wu, J.P. Xu, P.W. Crous, C. Jiao, H.Y. Li","doi":"10.3767/persoonia.2023.51.06","DOIUrl":"https://doi.org/10.3767/persoonia.2023.51.06","url":null,"abstract":"Species in<i> Diaporthe</i> have broad host ranges and cosmopolitan geographic distributions, occurring as endophytes, saprobes and plantpathogens. Previous studies have indicated that many<i> Diaporthe</i> species are associated with<i> Citrus</i>. To further determine the diversity\u0000of<i> Diaporthe</i> species associated with citrus diseases in China, we conducted extensive surveys in major citrus-producing are as from 2017–2020. Diseased tissues we recollected from leaves, fruits, twigs, branches and trunks showing a range of symptoms including melanose, dieback,\u0000gummosis, wood decay and canker. Based on phylogenetic comparisons of DNA sequences of the internal transcribed spacer regions(ITS), calmodulin(<i>cal</i>), histoneH3(<i>his3</i>), translation elongation factor1-alpha (<i>tef1</i>) and beta-tubulin (<i>tub2</i>), 393 isolates from 10 provinces\u0000were identified as belonging to 36 species of<i> Diaporthe</i>, including 32 known species, namely<i> D. apiculata</i>,<i> D. biconispora</i>,<i> D. biguttulata</i>,<i> D. caryae</i>,<i> D. citri</i>,<i> D. citriasiana</i>,<i> D. compacta</i>,<i> D. discoidispora</i>,<i> D. endophytica</i>,<i> D. eres</i>,<i> D. fusicola</i>,<i> D. fulvicolor</i>,<i> D. guangxiensis</i>,<i> D. hongkongensis</i>,<i> D. hubeiensis</i>,<i> D. limonicola</i>,<i> D. litchii</i>,<i> D. novem</i>,<i> D. passifloricola</i>,<i> D. penetriteum</i>,<i> D. pescicola</i>,<i> D. pometiae</i>,<i> D. sackstonii</i>,<i> D. sennicola</i>,<i> D. sojae</i>,<i> D. spinosa</i>,<i> D. subclavata</i>, <i>D. tectonae</i>,<i> D. tibetensis</i>,<i> D. unshiuensis</i>,<i> D. velutina</i> and<i> D. xishuangbanica</i>, and four new species, namely <i> D. gammata</i> ,<i> D. jishouensis</i>,<i> D. ruiliensis </i> and<i> D. sexualispora</i>. Among the 32 known species, 14 are reported for the first time on<i> Citrus</i>,<i> </i> and two are newly reported from China. Among the 36 species,<i> D. citri</i> was the dominant species as exemplified by its high frequency of isolationand virulence. Pathogenicity\u0000tests indicated that most<i> Diaporthe</i> species obtained in this study were weakly aggressive or non-pathogenic to the tested citrus varieties. Only<i> D. citri</i> produced the longest lesion lengths on citrus shoots and induced melanose on citrus leaves. These results further demonstrated\u0000that a rich diversity of<i> Diaporthe</i> species occupy<i> Citrus</i>, but only a few species are harmful and<i> D. citri </i> is the main pathogen for<i> Citrus</i> in China. The present study provides a basis from which targeted monitoring, prevention and control measures can be developed.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"25 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139584185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-31DOI: 10.3767/persoonia.2023.51.07
G.S. Li, C.A. Leal-Dutra, A. Cuesta-Maté, B.H. Conlon, N. Peereboom, C. Beemelmanns, D.K. Aanen, S. Rosendahl, Z.W. Debeer, M. Poulsen
Thegenus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises severals pecies, but their status is largely unresolved. Here we obtained basidiospores and photographs from166 fungarium specimens from around the world and generated a phylogeny basedonr DNA internal transcribed spacer ITS1, 5.8S and ITS2(ITS), and aphylogenomic analysis of 3839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on10 type specimens (holotype, paratype, andsyntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, orlectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five newspecies that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis.
林奈于 1771 年首次在印度描述了 Podaxis 属，但对该属的多次修订导致分类不清。目前有 44 个 Podaxis 种名和 9 个种内变种被接受，但大多数菌种标本都标为 Podaxis pistillaris。最近基于条形码基因的分子分析表明，该属由多个变种组成，但它们的地位在很大程度上尚未确定。在此，我们从世界各地的 166 个真菌标本中获得了基生孢子和照片，并根据rDNA 内部转录间隔 ITS1、5.8S 和 ITS2（ITS）生成了一个系统发育关系，还对其中一部分标本的低覆盖基因组中的 3839 个 BUSCO 基因进行了系统发生组分析。结合系统发生学、系统发生组学、形态学、生态学和地理分布，以及 250 年来的采集情况，我们认为该属至少包括 16 个明确的种。根据 10 个模式标本（主模式、副模式和综合模式），我们确认了 4 个记录在案的物种，分别是 P. carcinomalis、P. deflersii、P. emerici 和 P. farlowii。通过系统发育分析与描述的物种（包括形态学、生态学和分布）进行比较，我们复活了嗜白蚁属（P. termitophilus），并为五个先前描述的物种（P. aegyptiacus、P. africana、P. beringamensis、P. calyptratus 和 P. perraldieri）指定了新种、表型或选型。最后，根据系统发育和模式标本的形态，我们将已报道的三个种（P. algericus、P. arabicus 和 P. rugospora）与 P. pistillaris 同名，并描述了五个新种，分别命名为 P. desolatus、P. inyoensis、P. mareebaensis、P. namaquensis 和 P. namibensis。
{"title":"Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution","authors":"G.S. Li, C.A. Leal-Dutra, A. Cuesta-Maté, B.H. Conlon, N. Peereboom, C. Beemelmanns, D.K. Aanen, S. Rosendahl, Z.W. Debeer, M. Poulsen","doi":"10.3767/persoonia.2023.51.07","DOIUrl":"https://doi.org/10.3767/persoonia.2023.51.07","url":null,"abstract":"Thegenus<i> Podaxis</i> was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four<i> Podaxis</i> species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled<i> Podaxis pistillaris</i>. Recent molecular analyses based on barcoding genes suggest that the genus comprises severals pecies, but their status is largely unresolved. Here we obtained basidiospores and photographs from166 fungarium specimens from around the world and generated a phylogeny basedonr\u0000DNA internal transcribed spacer ITS1, 5.8S and ITS2(ITS), and aphylogenomic analysis of 3839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we\u0000propose that the genus includes at least 16 unambiguous species. Based on10 type specimens (holotype, paratype, andsyntype), four recorded species were confirmed,<i> P. carcinomalis</i>,<i> P. deflersii</i>,<i> P. emerici</i>, and<i> P. farlowii</i>. Comparing phylogenetic analysis with described\u0000species, including morphology, ecology, and distribution, we resurrected<i> P. termitophilus</i> and designated neotypes, epitypes, orlectotypes for five previously described species,<i> P. aegyptiacus</i>,<i> P. africana</i>,<i> P. beringamensis</i>,<i> P. calyptratus</i> and<i> P. perraldieri</i>.\u0000Lastly, based on phylogenies and morphology of type material, we synonymized three reported species,<i> P. algericus</i>,<i> P. arabicus</i>, and<i> P. rugospora</i> with<i> P. pistillaris</i>, and described five newspecies that we named<i> P. desolatus</i>,<i> P. inyoensis</i>,<i> P. mareebaensis</i>,<i> P. namaquensis</i>, and<i> P. namibensis</i>.","PeriodicalId":20014,"journal":{"name":"Persoonia","volume":"64 1","pages":""},"PeriodicalIF":9.1,"publicationDate":"2023-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139584298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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