Pub Date : 2024-07-01Epub Date: 2024-07-15DOI: 10.3114/sim.2024.108.01
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
<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
据估计，全球真菌的多样性在 200 万到 1100 万种之间，其中只有约 155 000 种已被命名。大多数真菌是肉眼看不见的，但它们却是地球生物多样性的主要组成部分，并发挥着重要的生态作用，支持着我们所知的生命。尽管目前已确认的真菌属大约有 2 万个，但大多数真菌的生态学仍未确定。尽管真菌种类繁多，但真菌学界对某些真菌属的研究却比其他真菌属更为活跃。这就提出了一个有趣的问题：为什么有些真菌属对真菌学及相关领域的影响比其他真菌属更大？为了解决这个问题，我们进行了文献计量分析，以确定被引用次数最多的前 100 个真菌属。我们对 Web of Science、Google Scholar 和 PubMed 进行了全面的数据库搜索，以确定哪些属的引用率最高。被引用最多的 10 个菌属分别是酵母菌属、念珠菌属、曲霉菌属、镰刀菌属、青霉属、毛霉菌属、灰霉属、毕赤菌属、隐球菌属和交替孢属。本文介绍了被引用次数最多的 100 个菌属的案例研究，包括一般背景、生态学和经济意义说明以及重要的研究进展。本文对这些菌属的科学研究进行了历史性概述，并展望了进一步研究的前景。引用：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、Takamatsu S、Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024).被引用最多的 100 个真菌属是什么？真菌学研究》108: 1-411. doi: 10.3114/sim.2024.108.01.
{"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}
Pub Date : 2024-03-01Epub Date: 2024-02-27DOI: 10.3114/sim.2024.107.04
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
<p><p>During 25 surveys of global <i>Phytophthora</i> 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 <i>Phytophthora</i> 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 <i>ca</i>. 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 <i>Phytophthora</i> clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single <i>Phytophthora</i> 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 <i>Phytophthora</i>. <b>Taxonomic novelties: New species:</b> <i>Phytophthora amamensis</i> T. Jung, K. Kageyama, H. Masuya & S. Uematsu, <i>Phytophthora angustata</i> T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, <i>Phytophthora balkanensis</i> I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, <i>Phytophthora borneensis</i> T. Jung, A. Durán, M. Tarigan & M. Horta Jung, <i>Phytophthora calidophila</i> T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, <i>Phytophthora catenulata</i> T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, <i>Phytophthora celeris</i> T. Jung, L. Oliveira, M. Tarigan & I. Milenković, <i>Phytophthora curvata</i> T. Jung, A. Hieno, H. Masuya & M.
在 1998 年至 2020 年期间进行的 25 次全球疫霉多样性调查中，在欧洲、东南亚、东亚和美洲的自然生态系统以及偶尔在苗圃和外植植物中发现了 43 个新物种。根据 9 个核基因区和 4 个线粒体基因区的多基因系统进化，它们被归入已知的 6 个亚支系中的 5 个，即 Phytophthora 主要支系 2 的 2a-c、e 和 f，以及新的亚支系 2g。该支系的进化史似乎涉及三个现存亚支系（2c、2e 和 2f）在鹅卵石万年前的分化，这三个亚支系都在不同的大陆上有不同的自然分布，包括生活方式为土生和水生的物种，此外，支系 2c 中还有一些部分为气生的物种；亚支系 2a 和 2g 在鹅卵石万年后分别在东南亚/东亚和南美洲从它们的共同祖先进化而来，支系 2b 在鹅卵石万年后从它们的共同祖先进化而来。支系 2g 中的物种在土壤中栖息，而支系 2b 则既包括在土壤中栖息的物种，也包括在空中栖息的物种。支系 2a 进一步向空中生活方式演化，只包括主要或部分在空中生活的物种。根据较高的核杂合度水平，2a 支系和 2b 支系中约 38% 的类群可能是某种形式的杂交种，A1/A2 繁殖系统和空中生活方式可能有利于这种杂交。间接证据表明，支系 2 中现已描述的 93 个物种和非正式指定的类群都是异地非适应性辐射和同地适应性辐射的结果。它们代表了整个噬菌属支系中的大多数形态和生理特征、繁殖系统、生活方式和寄主特化形式，显示了该属强大的生物凝聚力。在一个疫霉支系中发现了 43 个以前未知的物种，这凸显出在未知病原体对森林和自然生态系统的威胁程度方面严重缺乏信息，强调了主要根据命名生物清单制定植物生物安全协议的风险。需要在非洲、亚洲、中美洲和南美洲尚未调查的地区的自然生态系统中进行更多调查，以揭示该支系的全部多样性以及驱动疫霉菌多样性、物种和适应性的因素。分类学上的新发现：新物种：Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenković, Ž.Tomić, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora catenulata T. Jung, T.-T.T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenković, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung.Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M.Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora furcata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I.M. Milenković、Phytophthora indonesiensis T. Jung、M. Tarigan、L. Oliveira & I. Milenković、Phytophthora japonensis T. Jung、A. Hieno、H. Masuya & J.F. Webber、Phytophthora limosa T. Corcobado、T. Majek、M. Ferreira & T. Jung、Phytophthora macroglobulosa H.- C. Jung、Phytophthora macroglobulosa H.- J.F. Webber。C.Zeng, H.-H. Ho, F.-C.Ho, F.-C. Zheng & T. Jung, Phytophthora macroglobulosaZeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T.Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenković & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multiplex.Horta Jung、Phytophthora nimia T. Jung、H. Masuya、A. Hieno & C.M.Brasier、Phytophthora oblonga T. Jung、S. Uematsu、K. Kageyama & C.M.Brasier、Phytophthora obovoidea T. Jung、Y. Balc
{"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":"<p><p>During 25 surveys of global <i>Phytophthora</i> 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 <i>Phytophthora</i> 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 <i>ca</i>. 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 <i>Phytophthora</i> clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single <i>Phytophthora</i> 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 <i>Phytophthora</i>. <b>Taxonomic novelties: New species:</b> <i>Phytophthora amamensis</i> T. Jung, K. Kageyama, H. Masuya & S. Uematsu, <i>Phytophthora angustata</i> T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, <i>Phytophthora balkanensis</i> I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, <i>Phytophthora borneensis</i> T. Jung, A. Durán, M. Tarigan & M. Horta Jung, <i>Phytophthora calidophila</i> T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, <i>Phytophthora catenulata</i> T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, <i>Phytophthora celeris</i> T. Jung, L. Oliveira, M. Tarigan & I. Milenković, <i>Phytophthora curvata</i> 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}
Pub Date : 2024-03-01Epub Date: 2024-02-22DOI: 10.3114/sim.2024.107.03
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
<p><p>Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of <i>Fomitopsidaceae (Polyporales</i>, <i>Basidiomycota)</i>. After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, <i>viz</i>. <i>Anthoporia</i>, <i>Antrodia</i> and <i>Fomitopsis</i>. <i>Fomitopsis</i> becomes a large genus with 128 accepted species, containing almost all former <i>Fomitopsis</i> spp. and most species formerly placed in <i>Antrodia</i>, <i>Daedalea</i> and <i>Laccocephalum</i>. Genera <i>Buglossoporus</i>, <i>Cartilosoma</i>, <i>Daedalea</i>, <i>Melanoporia</i>, <i>Neolentiporus</i>, alongside twenty others, are treated as synonyms of <i>Fomitopsis</i>. This generic scheme allows for morphologically distinct genera in <i>Fomitopsidaceae</i>, unlike other schemes we considered. We provide arguments for retaining <i>Fomitopsis</i> and suppressing earlier (<i>Daedalea</i>, <i>Caloporus</i>) or simultaneously published generic names (<i>Piptoporus</i>) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + <i>TEF1</i>, ITS + <i>TEF1</i> + <i>RPB1</i> and ITS + <i>TEF1</i> + <i>RPB2</i> 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. <b>Taxonomic novelties: New species:</b> <i>Fomitopsis algumicola</i> Grebenc & Spirin, <i>F. caseosa</i> Vlasák & Spirin, <i>F. cupressicola</i> Vlasák, J. Vlasák Jr. & Spirin, <i>F. derelicta</i> Vlasák & Spirin, <i>F. dollingeri</i> Vlasák & Spirin, <i>F. fissa</i> Vlasák & Spirin, <i>F. lapidosa</i> Miettinen & Spirin, <i>F. lignicolor</i> Vlasák & Spirin, <i>F. maculosa</i> Miettinen & Spirin, <i>F. pannucea</i> Runnel & Spirin, <i>F. perhiemata</i> Viner & Spirin, <i>F. purpurea</i> Spirin & Ryvarden, <i>F. retorrida</i> Spirin & Kotiranta, <i>F. solaris</i> Rivoire, A.M. Ainsworth & Vlasák, <i>F. tristis</i> Miettinen & Spirin, <i>F. tunicata</i> Miettinen & Spirin, <i>F. visenda</i> Miettinen & Spirin. <b>New combinations:</b> <i>Fomitopsis aculeata</i> (Cooke) Spirin & Miettinen, <i>F. aethalodes</i> (Mont.) Spirin, <i>F. alaskana</i> (D.V. Baxter) Spirin & Vlasák, <i>F. albidoides</i> (A. David & Dequatre) Bernicchia & Vlasák, <i>F. amygdalina</i> (Berk. & Ravenel) Spirin & Vlasák, <i>F. angusta</i> (Spirin & Vlasák) Spirin & Vlasák, <i>F. atypa</i> (Lév.) Spirin & Vlasák, <i>F. caespitosa</i> (Murrill) Spirin & Miettinen, <i>F. calcitrosa</i> (Spirin & Miettinen) Spirin & Miettinen, <i>F. circularis</i> (B.K. Cui & Hai J. Li) Spirin, <i>F. concentrica</i> (G. Cunn.) M.D. Barrett, <i>F. cyclopis</i> (Miettinen & Spirin) Miettinen & Spirin, <i>F. dickinsii</i> (Berk. ex Cooke) Spirin, <i>F. elevata</i> (Corner) Spirin & Miettinen, <i>F. eucalypti</i> (Kalchbr.) Spirin, <i
tumulosa（Cooke）M.D. Barrett & Spirin，F. tuvensis（Spirin，Vlasák & Kotir.）Spirin & Vlasák，F. uralensis（Pilát）Spirin & Miettinen，F. ussuriensis（Bondartsev & Ljub.）Spirin & Miettinen，F. variiformis（Peck）Vlasák & Spirin，F. yunnanensis（M.L. Han & Q. An）Spirin，Daedaleopsis candicans（P. Karst.An) Spirin, Daedaleopsis candicans (P. Karst.) Spirin, Megasporoporia eutelea (Har. & Pat.) Spirin & Viner, Neofomitella hemitephra (Berk.) M.D. Barrett, Pseudophaeolus soloniensis (Dubois) Spirin & Rivoire, P. trichrous (Berk. & M.A. Curtis) Vlasák & Spirin.新异名：Antrodia bondartsevae Spirin, A. huangshanensis Y.C. Dai & B.K. Cui, A. taxa T.T. Chang & W.N. Chou, A. wangii Y.C. Dai & H.S. Yuan, Antrodiella subnigra Oba, Mossebo & Ryvarden, Antrodiopsis Audet, Boletus quercinus Schrad、Buglossoporus eucalypticola M.L. Han, B.K. Cui & Y.C. Dai, Caloporus P. Karst、Cartilosoma Kotlaba & Pouzar, Coriolus clemensiae Murrill, C. cuneatiformis Murrill, C. hollickii Murrill, C. parthenius Hariot & Pat., C. rubritinctus Murrill, Daedalea Pers、Daedalea allantoidea M.L. Han, B.K. Cui & Y.C. Dai, D. americana M.L. Han, Vlasák & B.K. Cui, D. radiata B.K. Cui & Hai J. Li, D. rajchenbergiana Kossmann & Drechsler-Santos, D. sinensis Lloyd.D. radiata B.K. Cui & Shun Liu, D. rajchenbergiana Kossmann & Drechler-Santos, D. sinensis Lloyd, Daedalella B.K. Cui & Shun Liu, Dentiporus Audet, Flavidoporia Audet, Fomes subferreus Murrill, Fomitopsis cana B.K. Cui, Hai J. Li & M.L. Han, F. caribensis B.K.Cui & Shun Liu, F. cystidiata B.K. Cui & M.L. Han, F. ginkgonis B.K. Cui & Shun Liu, F. iberica Melo & Ryvarden, F. incarnata K.M. Kim, J.S. Lee & H.S. Jung, F. subfeei B.K. Cui & M. M. L. Han, F. subropi B.K. Cui & M. L. Han.L. Han, F. subtropica B.K. Cui & Hai J. Li, Fragifomes B.K. Cui, M.L. Han & Y.C. Dai, Leptoporus epileucinus Pilát, Melanoporia Murrill, Neoantrodia Audet, Neolentiporus Rajchenb、Nigroporus macroporus Ryvarden & Iturr.，Niveoporofomes B.K. Cui, M.L. Han & Y.C. Dai，Pilatoporus Kotl、durescens Overh. ex J. Lowe, P. griseodurus Lloyd, Poria incarnata Pers、Rhodofomitopsis B.K. Cui, M.L. Han & Y.C. Dai, Rhodofomitopsis pseudofeei B.K. Cui & Shun Liu, R. roseomagna Nogueira-Melo, A.M.S. Soares & Gibertoni, Rubellofomes B. K. Cui, M.L. Han & Y.C. Dai, Rhodofomitopsis pseudofeei B.K. Cui & Shun Liu, R. roseomagna Nogueira-Melo, A.M.S. Soares & Gibertoni.K. Cui, M.L. Han & Y.C. Dai, Subantrodia Audet, Trametes fulvirubida Corner, T. lignea Murrill, T. lusor Corner, T. pseudodochmia Corner, T. subalutacea Bourdot & Galzin, T. supermodesta Ryvarden & Iturr、T. tuberculata Bres., Tyromyces multipapillatus Corner, T. ochraceivinosus Corner, T. palmarum Murrill, T. singularis Corner, T. squamosellus Núñez & Ryvarden, Ungulidaedalea B.K. Cui, M.L. Han & Y.C. Dai.Lectotypes：Hexagonia sulcata Berk.
{"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":"<p><p>Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of <i>Fomitopsidaceae (Polyporales</i>, <i>Basidiomycota)</i>. After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, <i>viz</i>. <i>Anthoporia</i>, <i>Antrodia</i> and <i>Fomitopsis</i>. <i>Fomitopsis</i> becomes a large genus with 128 accepted species, containing almost all former <i>Fomitopsis</i> spp. and most species formerly placed in <i>Antrodia</i>, <i>Daedalea</i> and <i>Laccocephalum</i>. Genera <i>Buglossoporus</i>, <i>Cartilosoma</i>, <i>Daedalea</i>, <i>Melanoporia</i>, <i>Neolentiporus</i>, alongside twenty others, are treated as synonyms of <i>Fomitopsis</i>. This generic scheme allows for morphologically distinct genera in <i>Fomitopsidaceae</i>, unlike other schemes we considered. We provide arguments for retaining <i>Fomitopsis</i> and suppressing earlier (<i>Daedalea</i>, <i>Caloporus</i>) or simultaneously published generic names (<i>Piptoporus</i>) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + <i>TEF1</i>, ITS + <i>TEF1</i> + <i>RPB1</i> and ITS + <i>TEF1</i> + <i>RPB2</i> 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. <b>Taxonomic novelties: New species:</b> <i>Fomitopsis algumicola</i> Grebenc & Spirin, <i>F. caseosa</i> Vlasák & Spirin, <i>F. cupressicola</i> Vlasák, J. Vlasák Jr. & Spirin, <i>F. derelicta</i> Vlasák & Spirin, <i>F. dollingeri</i> Vlasák & Spirin, <i>F. fissa</i> Vlasák & Spirin, <i>F. lapidosa</i> Miettinen & Spirin, <i>F. lignicolor</i> Vlasák & Spirin, <i>F. maculosa</i> Miettinen & Spirin, <i>F. pannucea</i> Runnel & Spirin, <i>F. perhiemata</i> Viner & Spirin, <i>F. purpurea</i> Spirin & Ryvarden, <i>F. retorrida</i> Spirin & Kotiranta, <i>F. solaris</i> Rivoire, A.M. Ainsworth & Vlasák, <i>F. tristis</i> Miettinen & Spirin, <i>F. tunicata</i> Miettinen & Spirin, <i>F. visenda</i> Miettinen & Spirin. <b>New combinations:</b> <i>Fomitopsis aculeata</i> (Cooke) Spirin & Miettinen, <i>F. aethalodes</i> (Mont.) Spirin, <i>F. alaskana</i> (D.V. Baxter) Spirin & Vlasák, <i>F. albidoides</i> (A. David & Dequatre) Bernicchia & Vlasák, <i>F. amygdalina</i> (Berk. & Ravenel) Spirin & Vlasák, <i>F. angusta</i> (Spirin & Vlasák) Spirin & Vlasák, <i>F. atypa</i> (Lév.) Spirin & Vlasák, <i>F. caespitosa</i> (Murrill) Spirin & Miettinen, <i>F. calcitrosa</i> (Spirin & Miettinen) Spirin & Miettinen, <i>F. circularis</i> (B.K. Cui & Hai J. Li) Spirin, <i>F. concentrica</i> (G. Cunn.) M.D. Barrett, <i>F. cyclopis</i> (Miettinen & Spirin) Miettinen & Spirin, <i>F. dickinsii</i> (Berk. ex Cooke) Spirin, <i>F. elevata</i> (Corner) Spirin & Miettinen, <i>F. eucalypti</i> (Kalchbr.) Spirin, <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}
Pub Date : 2023-11-01Epub Date: 2023-08-04DOI: 10.3114/sim.2023.106.03
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
Xerocomoideae is an ecologically and economically important Boletaceae subfamily (Boletales) comprising 10 genera. Although many studies have focused on Xerocomoideae in China, the diversity, taxonomy and molecular phylogeny still remained incompletely understood. In the present study, taxonomic and phylogenetic studies on Chinese species of Xerocomoideae were carried out by morphological examinations and molecular phylogenetic analyses. Eight genera in Xerocomoideae,viz.Aureoboletus,Boletellus,Heimioporus,Hemileccinum,Hourangia,Phylloporus,Pulchroboletus, andXerocomus 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 Bol. aff.putuoensis; two synonyms, viz.A. marroninus and P. dimorphus were defined. Among the Chinese accepted species, 13 were newly described, viz.A. albipes,A. conicus,A. ornatipes,Bol. erythrolepis, Bol. rubidus, Bol. sinochrysenteroides, Bol. subglobosus, Bol. zenghuoxingii,H. squamipes,P. hainanensis,Pul. erubescens,X. albotomentosus, andX. fuscatus, 36 known species were redescribed, and the other 48 species were reviewed. Keys to accepted species ofAureoboletus,Boletellus,Heimioporus,Hemileccinum,Hourangia,Phylloporus, andXerocomus in China were also provided. Taxonomic novelties: New species: Aureoboletus albipes N.K. Zeng, Xu Zhang & Zhi Q. Liang, A. conicus N.K. Zeng, Xu Zhang & Zhi Q. Liang, A. ornatipes N.K. Zeng, Xu Zhang & Zhi Q. Liang, Boletellus erythrolepis N.K. Zeng, R. Xue, S. Jiang & Zhi Q. Liang, Bol. rubidus N.K. Zeng, R. Xue, Y.J. Hao & Zhi Q. Liang, Bol. sinochrysenteroides N.K. Zeng, R. Xue & Kuan Zhao, Bol. subglobosus N.K. Zeng, R. Xue, S. Jiang & Zhi Q. Liang, Bol. zenghuoxingii N.K. Zeng, R. Xue, S. Jiang & Zhi Q. Liang, Hemileccinum squamipes N.K. Zeng, Chang Xu & Zhi Q. Liang, Phylloporus hainanensis N.K. Zeng, L.L. Wu, & Zhi Q. Liang, Pulchroboletus erubescens N.K. Zeng, Chang Xu & Zhi Q. Liang, Xerocomus albotomentosus N.K. Zeng, H.J. Xie, Chang Xu & Zhi Q. Liang, and X. fuscatus N.K. Zeng, H.J. Xie, Chang Xu & Zhi Q. Liang. Citation: 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 Xerocomoideae (Boletaceae, Boletales) in China. Studies in Mycology106: 95-197. doi: 10.3114/sim.2022.106.03.
{"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}
Pub Date : 2023-11-01Epub Date: 2023-08-15DOI: 10.3114/sim.2023.106.04
M Réblová, J Nekvindová
<p><p>In this study, we investigated the morphological and genetic variability of selected species belonging to the genus <i>Chloridium sensu lato</i>, 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 <i>Chaetosphaeriaceae</i> (<i>Chaetosphaeriales</i>) encompasses a wide range of asexual morphotypes, and among them, the simplest form is represented by <i>Chloridium</i> sect. <i>Chloridium</i>. The morphological simplicity of the <i>Chloridium</i> 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 <i>Chloridium</i> <i>sensu stricto</i> and can be grouped into two orders in the <i>Sordariomycetes</i>. Within the <i>Chaetosphaeriales</i>, they formed nine well-separated genera in four clades, such as <i>Cacumisporium</i>, <i>Caliciastrum gen. nov.</i>, <i>Caligospora gen. nov.</i>, <i>Capillisphaeria gen. nov.</i>, <i>Curvichaeta</i>, <i>Fusichloridium</i>, <i>Geniculoseta gen. nov.</i>, <i>Papillospora gen. nov.</i>, and <i>Spicatispora gen. nov.</i> We also established <i>Chloridiopsiella gen. nov.</i> and <i>Chloridiopsis gen. nov.</i> in <i>Vermiculariopsiellales</i>. Four new species and eight new combinations are proposed in these genera. Our study provides a clearer understanding of the genus <i>Chloridium</i>, 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. <b>Taxonomic novelties:</b> <b>New genera:</b> <i>Caliciastrum</i> Réblová, <i>Caligospora</i> Réblová, <i>Capillisphaeria</i> Réblová, <i>Chloridiopsiella</i> Réblová, <i>Chloridiopsis</i> Réblová, <i>Geniculoseta</i> Réblová, <i>Papillospora</i> Réblová, <i>Spicatispora</i> Réblová; <b>New species:</b> <i>Caliciastrum bicolor</i> Réblová, <i>Caligospora pannosa</i> Réblová, <i>Chloridiopsis syzygii</i> Réblová, <i>Gongromerizella silvana</i> Réblová; <b>New combinations:</b> <i>Caligospora dilabens</i> (Réblová & W. Gams) Réblová, <i>Capillisphaeria</i> <i>crustacea</i> (Sacc.) Réblová, <i>Chloridiopsiella preussii</i> (W. Gams & Hol.-Jech.) Réblová, <i>Chloridiopsis constrictospora</i> (Crous <i>et al</i>.) Réblová, <i>Geniculoseta preussii</i> (W. Gams & Hol.-Jech.) Réblová, <i>Papillospora hebetiseta</i> (Réblová & W. Gams) Réblová, <i>Spicatispora carpatica</i> (Hol.-Jech. & Révay) Réblová, <i>Spicatispora fennic
{"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":"<p><p>In this study, we investigated the morphological and genetic variability of selected species belonging to the genus <i>Chloridium sensu lato</i>, 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 <i>Chaetosphaeriaceae</i> (<i>Chaetosphaeriales</i>) encompasses a wide range of asexual morphotypes, and among them, the simplest form is represented by <i>Chloridium</i> sect. <i>Chloridium</i>. The morphological simplicity of the <i>Chloridium</i> 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 <i>Chloridium</i> <i>sensu stricto</i> and can be grouped into two orders in the <i>Sordariomycetes</i>. Within the <i>Chaetosphaeriales</i>, they formed nine well-separated genera in four clades, such as <i>Cacumisporium</i>, <i>Caliciastrum gen. nov.</i>, <i>Caligospora gen. nov.</i>, <i>Capillisphaeria gen. nov.</i>, <i>Curvichaeta</i>, <i>Fusichloridium</i>, <i>Geniculoseta gen. nov.</i>, <i>Papillospora gen. nov.</i>, and <i>Spicatispora gen. nov.</i> We also established <i>Chloridiopsiella gen. nov.</i> and <i>Chloridiopsis gen. nov.</i> in <i>Vermiculariopsiellales</i>. Four new species and eight new combinations are proposed in these genera. Our study provides a clearer understanding of the genus <i>Chloridium</i>, 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. <b>Taxonomic novelties:</b> <b>New genera:</b> <i>Caliciastrum</i> Réblová, <i>Caligospora</i> Réblová, <i>Capillisphaeria</i> Réblová, <i>Chloridiopsiella</i> Réblová, <i>Chloridiopsis</i> Réblová, <i>Geniculoseta</i> Réblová, <i>Papillospora</i> Réblová, <i>Spicatispora</i> Réblová; <b>New species:</b> <i>Caliciastrum bicolor</i> Réblová, <i>Caligospora pannosa</i> Réblová, <i>Chloridiopsis syzygii</i> Réblová, <i>Gongromerizella silvana</i> Réblová; <b>New combinations:</b> <i>Caligospora dilabens</i> (Réblová & W. Gams) Réblová, <i>Capillisphaeria</i> <i>crustacea</i> (Sacc.) Réblová, <i>Chloridiopsiella preussii</i> (W. Gams & Hol.-Jech.) Réblová, <i>Chloridiopsis constrictospora</i> (Crous <i>et al</i>.) Réblová, <i>Geniculoseta preussii</i> (W. Gams & Hol.-Jech.) Réblová, <i>Papillospora hebetiseta</i> (Réblová & W. Gams) Réblová, <i>Spicatispora carpatica</i> (Hol.-Jech. & Révay) Réblová, <i>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}
Pub Date : 2023-11-01Epub Date: 2023-07-19DOI: 10.3114/sim.2023.106.02
N Schoutteten, A Yurkov, O Leroux, D Haelewaters, D Van Der Straeten, O Miettinen, T Boekhout, D Begerow, A Verbeken
<p><p><b></b> Mycoparasites in <i>Basidiomycota</i> 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 <i>Microbotryomycetes</i> (<i>Pucciniomycotina</i>, <i>Basidiomycota</i>), 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 <i>Colacogloea</i>, the novel dimorphic mycoparasite <i>Mycogloiocolax gerardii</i>, and provide the first report of a sexual, mycoparasitic morph in <i>Colacogloea philyla</i> and in the genus <i>Slooffia</i>. 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 <i>Microbotryomycetes</i>. <b>Taxonomic novelties and typifications:</b> <b>New family:</b> <i>Mycogloiocolacaeae</i> Schoutteten & Yurkov; <b>New genus:</b> <i>Mycogloiocolax</i> Schoutteten & Rödel; <b>New species:</b> <i>Colacogloea bettinae</i> Schoutteten & Begerow, <i>C. biconidiata</i> Schoutteten, <i>C. fennica</i> Schoutteten & Miettinen, <i>C. microspora</i> Schoutteten, <i>C. universitatis-gandavensis</i> Schoutteten & Verbeken, <i>Mycogloiocolax gerardii</i> Schoutteten & Rödel; <b>New combinations:</b> <i>Slooffia micra</i> (Bourdot & Galzin) Schoutteten, <i>Fellozyma cerberi</i> (A.M. Yurkov <i>et al.</i>) Schoutteten & Yurkov, <i>Fellozyma telluris</i> (A.M. Yurkov <i>et al.</i>) Schoutteten & Yurkov; <b>Epitypifications (basionyms):</b> <i>Achroomyces insignis</i> Hauerslev, <i>Platygloea micra</i> Bourdot & Galzin, <i>Platygloea peniophorae</i> Bourdot & Galzin; <b>Lectotypification (basionym):</b> <i>Platygloea peniophorae</i> Bourdot & Galzin <b>Citation:</b> 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 <i>Microbotryomycetes</i>. <i>Studies in
基生真菌门中的寄生真菌包括形态和系统发育上多种多样的真菌。它们通过融合作用或菌胶团作用与宿主相互作用。菌胶体是真菌寄生虫在宿主-寄生虫界面上形成的亚细胞结构，可以穿透寄生虫和宿主的细胞壁。以前，通常通过透射电子显微镜在 19 种真菌中检测到过这种结构。大多数形成菌胶团的真菌被归入微囊霉菌纲（Pucciniomycotina，Basidiomycota），这是一类高度多样化的真菌，包括有袋酵母菌、霉菌寄生虫和植物寄生虫。一般来说，这些真菌寄生虫和植物寄生虫都是二态生物，具有寄生丝状形态和吸液酵母形态。我们以菌种材料、新鲜采集的标本和酵母菌形态的培养物为基础，对形成菌胶团的真菌寄生虫进行了研究。我们描述了丝状菌形态的微观形态、酵母菌形态的生理特征，并根据七个位点的 DNA 序列数据推断了系统发育关系。我们概述并采用了一种基于外荧光的显微方法来评估大肠体的存在和组织。我们描述了 Colacogloea 属中的五个新种、新型二态寄生菌 Mycogloiocolax gerardii，并首次报告了 Colacogloea philyla 和 Slooffia 属中的有性寄生菌形态。我们在 8 个真菌物种中检测到了菌胶体，从而使已知形成菌胶体的真菌总数达到 27 种。最后，我们在小袋真菌中发现了三种不同类型的菌胶体组织。新的分类和分型：新科：新科：Mycogloiocolacaeae Schoutteten & Yurkov；新属：Mycogloiocolax Schoutteten & Yurkov：新属：Mycogloiocolax Schoutteten & Rödel；新种：Colacogloea bettinae Schoutteten & Begerow, C. biconidiata Schoutteten, C. fennica Schoutteten & Miettinen, C. microspora Schoutteten, C. universitatis-gandavensis Schoutteten & Verbeken, Mycogloiocolax gerardii Schoutteten & Rödel; New combinations：Slooffia micra (Bourdot & Galzin) Schoutteten, Fellozyma cerberi (A.M. Yurkov et al.) Schoutteten & Yurkov, Fellozyma telluris (A.M. Yurkov et al.) Schoutteten & Yurkov; Epitypifications (basionyms)：Achroomyces insignis Hauerslev, Platygloea micra Bourdot & Galzin, Platygloea peniophorae Bourdot & Galzin; Lectotypification (basionym)：Platygloea peniophorae Bourdot & Galzin 引文：Schoutteten N, Yurkov A, Leroux O, Haelewaters D, Van Der Straeten D, Miettinen O, Boekhout T, Begerow D, Verbeken A (2023).与大肠菌群相互作用的寄生真菌的多样性拓展了对小袋真菌进化和生态学的认识。Doi: 10.3114/sim.2022.106.02.
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Pub Date : 2023-11-01Epub Date: 2023-07-17DOI: 10.3114/sim.2023.106.01
E Tanaka, K Tanada, T Hosoe, B Shrestha, M Kolařík, M Liu
Claviceps (Clavicipitaceae, Hypocreales) was erected in 1853, although ergotism had been well-known for a much longer time. By 2000, about 70 taxa had been described in Claviceps, of which eight species and six varieties were based on Japanese type or authentic specimens. Most of these Japanese Claviceps 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 Claviceps. 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, TEF-1α, TUB2, Mcm7, and RPB2 revealed the phylogenetic relationships between the Japanese specimens and known Claviceps spp., as well as the presence of biogeographic patterns. Based on the phylogenetic analysis, host range and morphology, we re-evaluated Japanese Claviceps and recognised at least 21 species in Japan. Here we characterised 14 previously described taxa and designated neo-, lecto- and epi-types for C. bothriochloae, C. imperatae, C. litoralis, C. microspora, C. panicoidearum and C. yanagawaensis. Two varieties were elevated to species rank with designated neotypes, i.e.C. agropyri and C. kawatanii. Six new species, C. miscanthicola, C. oplismeni, C. palustris, C. phragmitis, C. sasae and C. tandae were proposed and described. Taxonomic novelties:New species:Claviceps miscanthicola E. Tanaka, Claviceps oplismeni E. Tanaka, Claviceps palustris E. Tanaka, Claviceps phragmitis E. Tanaka, Claviceps sasae E. Tanaka, Claviceps tandae E. Tanaka; New status and combination:Claviceps agropyri (Tanda) E. Tanaka, Claviceps kawatanii (Tanda) E. Tanaka; Typifications (basionyms):Lecto- and epitypification:Claviceps yanagawaensis Togashi; Neotypifications: Claviceps purpurea var. agropyri Tanda, Claviceps bothriochloae Tanda & Y. Muray, Claviceps imperatae Tanda & Kawat., Claviceps microspora var. kawatanii Tanda, Claviceps litoralis Kawat., Claviceps microspora Tanda, Claviceps panicoidearum Tanda & Y. Harada; Resurrection: Claviceps queenslandica Langdon. Citation: Tanaka E, Tanada K, Hosoe T, Shrestha B, Kolařík M, Liu M (2023). In search of lost ergots: phylogenetic re-evaluation of Claviceps species in Japan and their biogeographic patterns revealed. Studies in Mycology106: 1-39. doi: 10.3114/sim.2022.106.01.
麦角菌（Clavicipitaceae，Hypocreales）于 1853 年被建立，尽管麦角菌在更长的时间内就已广为人知。到 2000 年，Claviceps 中已有约 70 个分类群被描述，其中 8 个种和 6 个变种是基于日本模式或真实标本。这些日本爪蟾分类群大多基于丢失的标本或无效名称，这意味着许多物种实际上只存在于科学文献中。这些物种的身份模糊不清，阻碍了姬蛙属分类学的研究。因此，我们寻找并采集了 300 多份新鲜标本，以寻找丢失的日本麦角。基于 LSU、TEF-1α、TUB2、Mcm7 和 RPB2 的 DNA 序列的多焦点系统发育分析揭示了日本标本与已知麦角属植物之间的系统发育关系，以及生物地理模式的存在。根据系统发育分析、寄主范围和形态学，我们重新评估了日本姬蛙，并确认日本至少有 21 个种。在这里，我们描述了 14 个以前描述过的类群的特征，并指定了 C. bothriochloae、C. imperatae、C. litoralis、C. microspora、C. panicoidearum 和 C. yanagawaensis 的新类型、变型和表型。Agropyri 和 C. kawatanii。提出并描述了六个新种：C. miscanthicola、C. oplismeni、C. palustris、C. phragmitis、C. sasae 和 C. tandae。新分类法：新物种：Claviceps miscanthicola E. Tanaka, Claviceps oplismeni E. Tanaka, Claviceps palustris E. Tanaka, Claviceps phragmitis E. Tanaka, Claviceps sasae E. Tanaka, Claviceps tandae E. Tanaka; 新地位和组合：Claviceps agropyri (Tanda) E. Tanaka, Claviceps kawatanii (Tanda) E. Tanaka; Typifications (basionyms)：Lecto- 和 epitypification：Claviceps yanagawaensis Togashi; Neotypifications：agropyri Tanda, Claviceps bothriochloae Tanda & Y. Muray, Claviceps impermidi.Muray, Claviceps imperatae Tanda & Kawat：Claviceps queenslandica Langdon.引用：Tanaka E, Tanada K, Hosoe T, Shrestha B, Kolařík M, Liu M (2023).寻找失落的麦角：日本麦角属物种的系统发育再评价及其生物地理模式揭示。Doi: 10.3114/sim.2022.106.01.
{"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}
Pub Date : 2023-07-01Epub Date: 2023-02-22DOI: 10.3114/sim.2022.104.02
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
Fusarium 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 Fusarium 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 Fusarium 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 Fusarium 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 Fusarium 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 Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties:New species:Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology104: 87-148. doi: 10.3114/sim.2022.104.02.
镰刀菌是重要的谷物病原体，对玉米、水稻和小麦等主要谷物作物造成严重的产量损失。然而，谷物上镰刀菌病害的病原菌还没有被很好地记录下来，原因是很难进行物种鉴定，而且围绕着属种和种的概念还存在争议。在本研究中，我们利用公民科学计划调查了中国主要谷物种植区 250 个地点的患病谷物作物（玉米、水稻和小麦）。从 315 个病害样本中共分离出 2 020 株镰刀菌。通过多焦点系统发育和形态特征，上述菌株被鉴定为 43 个种，其中包括本文描述的 8 个新种。本文提供了与谷物相关的镰刀菌种的世界清单，分别更新了世界和中国的 39 条和 52 条新记录。值得注意的是，在本研究中采集的样本中有 56% 同时感染了一种以上的镰刀菌，并对其详细的关联进行了讨论。根据科赫假说，本研究首次确认了 18 个菌种为玉米茎腐病的病原体。此外，本研究还根据 228 个组装基因组（本研究提供了 40 个基因组的测序结果）的 1 001 个同源位点构建了高置信度的物种树，支持镰刀菌（=吉伯菌）的 "狭义 "属概念。这项研究是迄今为止对谷物镰刀菌病害最全面的调查之一。它极大地提高了我们对谷物相关镰刀菌物种的全球多样性和分布的认识，并在很大程度上澄清了该属内部的系统发育关系。分类学上的新发现：新种：Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium notanense S.L. Han, M.M. Wang & L. Cai.Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai.引用：Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023).与中国病害谷物相关的镰刀菌多样性，以及对该属系统发生组的最新评估。Doi: 10.3114/sim.2022.104.02.
{"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}
L G Nagy, P J Vonk, M Künzler, C Földi, M Virágh, R A Ohm, F Hennicke, B Bálint, Á Csernetics, B Hegedüs, Z Hou, X B Liu, S Nan, M Pareek, N Sahu, B Szathmári, T Varga, H Wu, X Yang, Z Merényi
<p><p>Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (<i>Agaricomycetes</i>) 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 <i>Coprinopsis cinerea</i>, and their orthologs in <i>Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus</i>, and <i>Schizophyllum commune</i>, 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 <i>Agaricomycetes</i>. 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. <b>Citation:</b> 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 <i>Agaricomycetes. Studies in Mycology</i> <b>104</b>: 1-85. doi: 10
成菇真菌的子实体(孢子囊、孢子或担子瘤)是真菌产生的最复杂的结构之一。与营养菌丝不同，子实体的生长是决定性的，并遵循遗传编码的发育程序，协调它们的生长、组织分化和性孢子形成。尽管经过一个多世纪的研究，我们对子实体形态发生的分子细节的了解仍然有限，缺乏对这一复杂过程的遗传学综合。在本文中，我们旨在全面鉴定与子实体形态发生有关的保守基因，并对功能不明确的基因提出新的功能假设。根据这一分析结果，我们报道了921个保守的发育表达基因家族，其中只有几十个先前被报道参与子实体发育。基于文献数据、保守表达模式和功能注释，我们对这些基因家族在子实体发育中的潜在作用提出了假设，得到了迄今为止最完整的子实体形态发生分子过程描述。我们讨论了与结果、分化、生长、细胞表面和细胞壁、防御、转录调控以及信号转导有关的基因。基于这些数据，我们得出了子实体发育的一般模型，其中包括早期的增殖阶段，主要涉及制定蘑菇体计划(通过细胞分裂和分化)，以及通过细胞扩增以及减数分裂事件和产孢的第二阶段生长。我们总共讨论了1 480个铜opsis cinerea的基因，以及它们在双孢蘑菇(Agaricus bisporus)、绿环菌(Cyclocybe aegerita)、蜜环菌(Armillaria ostoyae)、耳虫(Auriculariopsis ampla)、双色乳酸菌(Laccaria bicolor)、香菇(Lentinula edodes)、香菇(lentus tigrinus)、肯特菌(Mycena kentingensis)、黄孢平革菌(Phanerochaete chrysporium)、平菇(Pleurotus ostreatus)和裂叶菌(Schizophyllum commune)中的同源基因，为这些物种基因组中约10%的基因提供了功能假设。虽然这些基因作用的实验证据需要在未来建立，但我们的数据为指导真菌中结果相关基因的功能分析提供了路线图。我们预计，这里提出的基因纲要，结合功能基因组学方法的发展，将有助于揭示真菌中最壮观的多细胞发育过程之一的遗传基础。引用本文:Nagy LG, Vonk PJ, k zler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, csertics Á， heged S B，侯志，刘小斌，Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T，吴伟，杨旭，mersamnyi Z(2023)。菌丝体基因组和转录组对子实体形态发生的启示。真菌学研究104:1-85。doi: 10.3114 / sim.2022.104.01。
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Pub Date : 2023-06-01Epub Date: 2023-05-25DOI: 10.3114/sim.2023.105.01
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
<p><p>The subphylum <i>Saccharomycotina</i> is a lineage in the fungal phylum <i>Ascomycota</i> that exhibits levels of genomic diversity similar to those of plants and animals. The <i>Saccharomycotina</i> 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 <i>Saccharomycotina</i> has much higher rates of genome sequence evolution than its sister subphylum, <i>Pezizomycotina</i>, it contains only one class compared to the 16 classes in <i>Pezizomycotina</i>. The third subphylum of <i>Ascomycota</i>, the <i>Taphrinomycotina</i>, consists of six classes and has approximately 10 times fewer species than the <i>Saccharomycotina</i>. 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 <i>Saccharomycotina</i> contains 12 major and robustly supported phylogenetic clades; seven of these are current families (<i>Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae</i>, and <i>Saccharomycetaceae</i>), one comprises two current families (<i>Dipodascaceae</i> and <i>Trichomonascaceae</i>), one represents the genus <i>Sporopachydermia</i>, 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 <i>Saccharomycotina</i>, 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 <i>Saccharomycotina</i> more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. <b>Taxonomic novelties: New classes:</b> <i>Alloascoideomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Dipodascomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Lipomycetes</i> M. Groenew., Hittinger, Opulente, A. Rokas, <i>Pichiomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Sporopachydermiomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Trigonopsidomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas. <b>New orders:</b> <i><b>Alloascoideomycetes:</b></i> <i>Alloascoideales</i> M. Groenew., Hittinger, Opulente & A. Rokas; <i><b>Di
酵母菌亚门（subphylum Saccharomycotina）是真菌门（Ascomycota）中的一个分支，其基因组多样性水平与动植物相似。酵母菌亚门目前有 1200 多个已知物种，分为 16 科、1 目和 1 类。该亚门中的物种在生态和新陈代谢方面具有多样性，包括重要的人类机会性病原体以及在生物技术应用中非常重要的物种。许多具有生物技术意义的性状都存在于近缘物种中，而且往往局限于单一的系统发育支系。然而，大多数酵母物种的生物技术潜力仍有待开发。虽然酵母亚门的基因组序列进化速度远高于其姊妹亚门 Pezizomycotina，但与 Pezizomycotina 的 16 个类别相比，酵母亚门只包含一个类别。Ascomycota 的第三个亚门，Taphrinomycotina，包括 6 个类别，其物种数量大约是 Saccharomycotina 的 10 倍。这些数据表明，目前将所有这些酵母菌分为一个类和一个目是对其多样性的低估。我们之前进行的基因组规模的系统发育分析表明，酵母菌纲包含 12 个主要的、得到强有力支持的系统发育支系；其中 7 个是现存的科（唇形科、三叉科、藻类学科、藻类学科、藻类学科、酵母菌科和酵母菌科）、一个代表目前的两个科（Dipodascaceae 和 Trichomonascaceae），一个代表 Sporopachydermia 属，三个代表在翻译 CUG 密码子（CUG-Ala、CUG-Ser1 和 CUG-Ser2）时不同的品系。通过这些分析以及相对进化差异和基因组含量分析，我们提出了酵母菌纲的最新分类方法，包括可通过基因组含量进行诊断的 7 类和 12 目。这一更新的分类与该亚门中基因组的高度多样性相一致，而且对于使酵母菌亚门的高等级分类与其他真菌的高等级分类更具有可比性，以及对尚未正式命名的世系进行有效交流是必要的。新分类法：新类别：Alloascoideomycetes M. Groenew.Rokas, Dipodascomycetes M. Groenew.Rokas, Lipomycetes M. Groenew.Rokas, Sporopachydermiomycetes M. Groenew.Rokas, Trigonopsidomycetes M. Groenew.Rokas.New orders：Alloascoideomycetes：Alloascoideales M. Groenew.Rokas; Dipodascomycetes：Dipodascales M. Groenew.Rokas; Lipomycetes：Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew.Rokas; Pichiomycetes：Alaninales M. Groenew.Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew.Rokas, Serinales M. Groenew.Rokas; Saccharomycetes：M.Groenew.、Hittinger、Opulente & A. Rokas；Saccharomycetes: Phaffomycetales M. Groenew.Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew.Rokas; Sporopachydermiomycetes：Sporopachydermiales M. Groenew.Rokas; Trigonopsidomycetes：Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew.Rokas.New families：Alaninales：新科：Alaninales: Pachysolenaceae M. Groenew.Rokas; Pichiales：Pichiaceae M. Groenew.Rokas; Sporopachydermiales：Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew.Rokas.引用：Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA、Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023).具有重要生物技术价值的真菌亚门酵母菌的基因组信息高等级分类。Doi: 10.3114/sim.2023.105.01 本研究献给酵母分类学先驱 Cletus P. Kurtzman（1938-2017 年）。
{"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":"<p><p>The subphylum <i>Saccharomycotina</i> is a lineage in the fungal phylum <i>Ascomycota</i> that exhibits levels of genomic diversity similar to those of plants and animals. The <i>Saccharomycotina</i> 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 <i>Saccharomycotina</i> has much higher rates of genome sequence evolution than its sister subphylum, <i>Pezizomycotina</i>, it contains only one class compared to the 16 classes in <i>Pezizomycotina</i>. The third subphylum of <i>Ascomycota</i>, the <i>Taphrinomycotina</i>, consists of six classes and has approximately 10 times fewer species than the <i>Saccharomycotina</i>. 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 <i>Saccharomycotina</i> contains 12 major and robustly supported phylogenetic clades; seven of these are current families (<i>Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae</i>, and <i>Saccharomycetaceae</i>), one comprises two current families (<i>Dipodascaceae</i> and <i>Trichomonascaceae</i>), one represents the genus <i>Sporopachydermia</i>, 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 <i>Saccharomycotina</i>, 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 <i>Saccharomycotina</i> more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. <b>Taxonomic novelties: New classes:</b> <i>Alloascoideomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Dipodascomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Lipomycetes</i> M. Groenew., Hittinger, Opulente, A. Rokas, <i>Pichiomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Sporopachydermiomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas, <i>Trigonopsidomycetes</i> M. Groenew., Hittinger, Opulente & A. Rokas. <b>New orders:</b> <i><b>Alloascoideomycetes:</b></i> <i>Alloascoideales</i> M. Groenew., Hittinger, Opulente & A. Rokas; <i><b>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}
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