Ima FungusPub Date : 2024-08-13DOI: 10.1186/s43008-024-00159-4
Brigida Gallone, Thomas W Kuyper, Jorinde Nuytinck
{"title":"The genus Cortinarius should not (yet) be split.","authors":"Brigida Gallone, Thomas W Kuyper, Jorinde Nuytinck","doi":"10.1186/s43008-024-00159-4","DOIUrl":"10.1186/s43008-024-00159-4","url":null,"abstract":"<p><p>The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11321212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977224","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}
Ima FungusPub Date : 2024-08-07DOI: 10.1186/s43008-024-00157-6
Wan Ting Yu, Xin Wang, Tan Yin, Clement Kin-Ming Tsui, Chong Juan You
{"title":"Development and validation of a rapid loop-mediated isothermal amplification assay for the detection of Chrysomyxa and characterization of Chrysomyxa woroninii overwintering on Picea in China.","authors":"Wan Ting Yu, Xin Wang, Tan Yin, Clement Kin-Ming Tsui, Chong Juan You","doi":"10.1186/s43008-024-00157-6","DOIUrl":"10.1186/s43008-024-00157-6","url":null,"abstract":"<p><p>Chrysomyxa rusts cause significant damage to spruce in both natural forests and plantations. Particularly, Three Chrysomyxa species, Chrysomyxa deformans, Chrysomyxa qilianensis, and Chrysomyxa rhododendri, listed as National Forest Dangerous Pests in China, have severely affected many economically and ecologically important spruce native species in China. Also, Chrysomyxa arctostaphyli, an important plant quarantine fungus, causes a damaging broom rust disease on spruce. Therefore, rapid, and efficient detection tools are urgently needed for proper rust disease detection and management. In this study, a sensitive, genus-specific loop-mediated isothermal amplification (LAMP) assay targeting the ITS-28S rRNA region was developed to detect the presence of Chrysomyxa in spruce needle and bud samples. After optimization and validation, the LAMP assay was found to be sensitive to detect as low as 5.2 fg/µL DNA, making it suitable for rapid on-site testing for rust infection. The assay was also specific to Chrysomyxa species, with no positive signals from other rust genus/species. The application of LAMP in the early detection of rust infections in spruce needles and buds was investigated, and spatial colonization profiles as well as the means of overwintering of Chrysomyxa woroninii in infected buds and branches were verified using the LAMP assay. This LAMP detection method will facilitate further studies on the characteristics of the life cycle and inoculation of other systemic rusts.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11304928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903604","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}
Ima FungusPub Date : 2024-08-05DOI: 10.1186/s43008-024-00156-7
Julia Prakofjewa, Matteo Sartori, Raivo Kalle, Łukasz Łuczaj, Małgorzata Karbarz, Giulia Mattalia, Povilas Šarka, Baiba Prūse, Nataliya Stryamets, Martin Anegg, Natalia Kuznetsova, Valeria Kolosova, Olga Belichenko, Muhammad Abdul Aziz, Andrea Pieroni, Renata Sõukand
{"title":"\"But how true that is, I do not know\": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union.","authors":"Julia Prakofjewa, Matteo Sartori, Raivo Kalle, Łukasz Łuczaj, Małgorzata Karbarz, Giulia Mattalia, Povilas Šarka, Baiba Prūse, Nataliya Stryamets, Martin Anegg, Natalia Kuznetsova, Valeria Kolosova, Olga Belichenko, Muhammad Abdul Aziz, Andrea Pieroni, Renata Sõukand","doi":"10.1186/s43008-024-00156-7","DOIUrl":"10.1186/s43008-024-00156-7","url":null,"abstract":"<p><p>Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894887","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}
Ima FungusPub Date : 2024-07-25DOI: 10.1186/s43008-024-00153-w
Mohamed Taha, Yasmine H Tartor, Rana M Abd Elaziz, Ibrahim Elsohaby
{"title":"Genetic diversity and antifungal susceptibilities of environmental Cryptococcus neoformans and Cryptococcus gattii species complexes.","authors":"Mohamed Taha, Yasmine H Tartor, Rana M Abd Elaziz, Ibrahim Elsohaby","doi":"10.1186/s43008-024-00153-w","DOIUrl":"10.1186/s43008-024-00153-w","url":null,"abstract":"<p><p>Cryptococcosis is an opportunistic systemic mycosis caused by Cryptococcus neoformans and C. gattii species complexes and is of increasing global importance. Maintaining continued surveillance of the antifungal susceptibility of environmental C. neoformans and C. gattii isolates is desirable for better managing cryptococcosis by identifying resistant isolates and revealing the emergence of intrinsically resistant species. Relevant research data from Egypt are scarce. Thus, this study aimed to report the genetic diversity of C. neoformans and C. gattii species complexes originating from different environmental sources in Egypt, antifungal susceptibility profiles, antifungal combinations, and correlations of susceptibility with genotypes. A total of 400 environmental samples were collected, 220 from birds and 180 from trees. Cryptococcus spp. were found in 58 (14.5%) of the samples, 44 (75.9%) of the isolates were recovered from birds and 14 (24.1%) from trees. These isolates were genotyped using M13 polymerase chain reaction-fingerprinting and URA5 gene restriction fragment length polymorphism analysis. Of the 31 C. neoformans isolates, 24 (77.4%), 6 (19.4%) and one (4.4%) belonged to VNI, VNII, and VNIII genotypes, respectively. The 27 C. gattii isolates belonged to VGI (70.4%), VGII (18.5%), and VGIII (11.1%) genotypes. Non-wild type C. neoformans and C. gattii isolates that may have acquired resistance to azoles, amphotericin B (AMB), and terbinafine (TRB) were observed. C. gattii VGIII was less susceptible to fluconazole (FCZ) and itraconazole (ITZ) than VGI and VGII. C. neoformans isolates showed higher minimum inhibitory concentrations (MICs) to FCZ, ITZ, and voriconazole (VRZ) than those of C. gattii VGI and VGII. Significant (P < 0.001) correlations were found between the MICs of VRZ and ITZ (r = 0.64) in both C. neoformans and C. gattii isolates, FCZ and TRB in C. neoformans isolates, and FCZ and TRB (r = 0.52) in C. gattii isolates.There is no significant differences in the MICs of TRB in combination with FCZ (P = 0.064) or in combination with AMB (P = 0.543) and that of TRB alone against C. gattii genotypes. By calculating the fractional inhibitory concentration (FIC) index, the combination of FCZ + AMB was synergistic against all tested genotypes. These findings expand our knowledge of ecological niches, genetic diversity, and resistance traits of C. neoformans and C. gattii genotypes in Egypt. Further investigations into how they are related to clinical isolates in the region are warranted.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141768077","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}
Ima FungusPub Date : 2024-07-24DOI: 10.1186/s43008-024-00155-8
Andrey Yurkov, Cobus M Visagie, Pedro W Crous, Akira Hashimoto, Christiane Baschien, Dominik Begerow, Martin Kemler, Nathan Schoutteten, Marc Stadler, Nalin N Wijayawardene, Kevin D Hyde, Ning Zhang, Teun Boekhout, Tom W May, Marco Thines, David L Hawksworth
{"title":"Cultures as types and the utility of viable specimens for fungal nomenclature.","authors":"Andrey Yurkov, Cobus M Visagie, Pedro W Crous, Akira Hashimoto, Christiane Baschien, Dominik Begerow, Martin Kemler, Nathan Schoutteten, Marc Stadler, Nalin N Wijayawardene, Kevin D Hyde, Ning Zhang, Teun Boekhout, Tom W May, Marco Thines, David L Hawksworth","doi":"10.1186/s43008-024-00155-8","DOIUrl":"10.1186/s43008-024-00155-8","url":null,"abstract":"<p><p>The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11267820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762659","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}
Ima FungusPub Date : 2024-07-24DOI: 10.1186/s43008-024-00150-z
James K Mitchell, David L Hawksworth, Shaun R Pennycook
{"title":"Report of the Special-purpose Committee on Names of Fungi with the Same Epithet, established at the XIX International Botanical Congress in Shenzhen, China.","authors":"James K Mitchell, David L Hawksworth, Shaun R Pennycook","doi":"10.1186/s43008-024-00150-z","DOIUrl":"10.1186/s43008-024-00150-z","url":null,"abstract":"<p><p>A Special-purpose Committee on Fungal Names with the Same Epithet was established at the XIX International Botanical Congress (IBC) in Shenzhen, China in 2017, with a mandate to report to the 12th International Mycological Congress (IMC) with recommendations on a preferred course of action with respect to names of pleomorphic fungi sharing the same epithet under the International Code of Nomenclature for algae, fungi, and plants. This report provides a synthesis of the deliberations from the Special-purpose Committee. We discuss the arguments for and against the proposed solution to the problems that have arisen regarding the nomenclature of fungi described in multiple morphs using the same epithet. We also propose a gentler method of addressing the problem using existing procedures.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11267818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762660","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}
Ima FungusPub Date : 2024-07-03DOI: 10.1186/s43008-024-00145-w
Paula Andrea Gómez-Zapata, Jorge Ronny Díaz-Valderrama, Samira Fatemi, Cristhian Orlando Ruiz-Castro, M Catherine Aime
{"title":"Characterization of the fungal genus Sphaerellopsis associated with rust fungi: species diversity, host-specificity, biogeography, and in-vitro mycoparasitic events of S. macroconidialis on the southern corn rust, Puccinia polysora.","authors":"Paula Andrea Gómez-Zapata, Jorge Ronny Díaz-Valderrama, Samira Fatemi, Cristhian Orlando Ruiz-Castro, M Catherine Aime","doi":"10.1186/s43008-024-00145-w","DOIUrl":"10.1186/s43008-024-00145-w","url":null,"abstract":"<p><p>Sphaerellopsis species are putative hyperparasites of rust fungi and may be promising biological control agents (BCA) of rust diseases. However, few detailed studies limit potential BCA development in Sphaerellopsis. Here, we explored the biogeography, host-specificity, and species diversity of Sphaerellopsis and examined the early infection stage of one species, S. macroconidialis, to infer its trophic status. We randomly screened 5,621 rust specimens spanning 99 genera at the Arthur Fungarium for the presence of Sphaerellopsis. We identified 199 rust specimens infected with Sphaerellopsis species on which we conducted morphological and multi-locus phylogenetic analyses. Five Sphaerellopsis species were recovered, infecting a total of 122 rust species in 18 genera from 34 countries. Sphaerellopsis melampsorinearum sp. nov. is described as a new species based on molecular phylogenetic data and morphological features of the sexual and asexual morphs. Sphaerellopsis paraphysata was the most commonly encountered species, found on 77 rust specimens, followed by Sphaerellopsis macroconidialis on 56 and S. melampsorinearum on 55 examined specimens. The type species, Sphaerellopsis filum, was found on 12 rust specimens and Sphaerellopsis hakeae on a single specimen. We also recovered and documented for the first time, the sexual morph of S. macroconidialis, from a specimen collected in Brazil. Our data indicate that Sphaerellopsis species are not host specific and furthermore that most species are cosmopolitan in distribution. However, S. paraphysata is more abundant in the tropics, and S. hakeae may be restricted to Australia. Finally, we confirm the mycoparasitic strategy of S. macroconidialis through in-vitro interaction tests with the urediniospores of Puccinia polysora. Shortly after germination, hyphae of S. macroconidialis began growing along the germ tubes of P. polysora and coiling around them. After 12 days of co-cultivation, turgor loss was evident in the germ tubes of P. polysora, and appressorium-like structures had formed on urediniospores. The interaction studies indicate that Sphaerellopsis species may be more effective as a BCA during the initial stages of rust establishment.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11223437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499647","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}
Ima FungusPub Date : 2024-06-27DOI: 10.1186/s43008-024-00144-x
Vedprakash G Hurdeal, Joyce E Longcore, E B Gareth Jones, Kevin D Hyde, Eleni Gentekaki
{"title":"Diversity of Rhizophydiales (Chytridiomycota) in Thailand: unveiling the hidden gems of the Kingdom.","authors":"Vedprakash G Hurdeal, Joyce E Longcore, E B Gareth Jones, Kevin D Hyde, Eleni Gentekaki","doi":"10.1186/s43008-024-00144-x","DOIUrl":"https://doi.org/10.1186/s43008-024-00144-x","url":null,"abstract":"<p><p>Chytrids, often overshadowed by their other fungal counterparts, take center stage as we unravel the mysteries surrounding new species within Rhizophydiales and explore their unique characteristics. In the broader spectrum of chytrids, their significance lies not only in their roles as decomposers but also as key players in nutrient cycling within aquatic ecosystems as parasites and saprobes. Baited soil and aquatic samples collected from various provinces of Thailand, yielded new species of the Rhizophydiales (Chytridiomycota), some of which expanded previously single species genera. Our investigation incorporated a combination of morphological and phylogenetic approaches, enabling us to identify these isolates as distinct taxa. The novel isolates possess distinguishing features, such as variations in size and shape of the sporangium and zoospores, that somewhat differentiate them from described taxa. To confirm the novelty of the species, we employed robust phylogenetic analyses using maximum likelihood and bayesian methods. The results provided strong support for the presence of eight distinct lineages within the Rhizophydiales, representing our newly discovered species. Furthermore, we employed Poisson Tree Processes to infer putative species boundaries and supplement evidence for the establishment of our new Rhizophydiales species. By meticulously exploring their morphological characteristics and genetic makeup, we expand the known catalogue of fungal diversity by describing Alphamyces thailandicus, Angulomyces ubonensis, Gorgonomyces aquaticus, G. chiangraiensis, G. limnicus, Pateramyces pingflumenensis, Terramyces aquatica, and T. flumenensis and also provide valuable insights into the intricacies of this order. This newfound knowledge not only enriches our understanding of Rhizophydiales but also contributes significantly to the broader field of mycology, addressing a critical gap in the documentation of fungal species. The identification and characterization of these eight novel species mark a noteworthy stride towards a more comprehensive comprehension of fungal ecosystems and their vital role.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472600","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}
Ima FungusPub Date : 2024-06-24DOI: 10.1186/s43008-024-00148-7
Cony Decock, Milay Cabarroi-Hernández, Laura Guzmán-Dávalos, Paul M Kirk, José Ángel García-Beltrán, Mario Amalfi
{"title":"Fomes weberianus, 50 years of taxonomic confusion: lectotypification and taxonomic notes.","authors":"Cony Decock, Milay Cabarroi-Hernández, Laura Guzmán-Dávalos, Paul M Kirk, José Ángel García-Beltrán, Mario Amalfi","doi":"10.1186/s43008-024-00148-7","DOIUrl":"10.1186/s43008-024-00148-7","url":null,"abstract":"<p><p>Fomes weberianus Bres. & Henn. ex Sacc. is currently the basionym of two very distinct polypores (Basidiomycota), Ganoderma weberianum (Polyporales) and Phylloporia weberiana (Hymenochaetales). This fact has led to almost fifty years of taxonomic confusion. Fomes weberianus was first lectotypified by Steyaert, who accepted the species as G. weberianum. However, studies of Weber's original material in B, duplicate material in S, the protologue, and early interpretations of the name have shown that Steyaert's choice conflicts with the protologue and early interpretations, and that his interpretation as a species of Ganoderma is erroneous. A new lectotype was designated and the species was re-described under the correct interpretation Phylloporia weberiana.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11194980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny.","authors":"Xinzheng Song, Yuehua Geng, Chao Xu, Jiaxin Li, Yashuang Guo, Yan Shi, Qingzhou Ma, Qiang Li, Meng Zhang","doi":"10.1186/s43008-024-00149-6","DOIUrl":"10.1186/s43008-024-00149-6","url":null,"abstract":"<p><p>In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":null,"pages":null},"PeriodicalIF":5.4,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11167856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307431","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}