Mycological Progress最新文献_第7页

The TrEase web service: inferring phylogenetic trees with ease TrEase web服务:轻松推断系统发育树

IF 2.4 3区生物学

Mycological Progress Pub Date : 2023-11-23 DOI: 10.1007/s11557-023-01931-3

Bagdevi Mishra, Sebastian Ploch, Claus Weiland, Marco Thines

{"title":"The TrEase web service: inferring phylogenetic trees with ease","authors":"Bagdevi Mishra, Sebastian Ploch, Claus Weiland, Marco Thines","doi":"10.1007/s11557-023-01931-3","DOIUrl":"https://doi.org/10.1007/s11557-023-01931-3","url":null,"abstract":"Phylogenetic inference is done regularly in many biological studies not focussed on the phylogeny itself, but which use phylogeny as a tool to infer hypotheses for the interpretation of laboratory experiments. However, phylogenetic inference is often performed at low standards in these studies, which can result in wrong interpretations. Using high-standard phylogenetic inference tools usually requires substantial methodological knowledge or is only possible with paid tools. To enable beginners, researchers for which phylogeny is just one tool of many, and scientists in biodiversity discovery a quick and easy access to current phylogenetic methods, the TrEase web service with an intuitive interface was developed. It offers a complete pipeline with commonly used phylogeny-related software, which can run the whole process of sequence acquisition, reference sequence search, alignment and phylogenetic inference with a single execution command once the necessary parameters have been selected from drop-down menus. It allows choosing alternate programmes for each step and also offers the flexibility to use any part of the pipeline independently. Along with providing a compact pipeline, this web service provides several functionalities to avoid manual intervention such as sorting sequences into the same orientation, cutting reference sequences, removal of redundant sequences and the possibility to choose reference sequences from top ‘species’ hits instead of top GenBank entry hits. All resulting trees and intermediate files are made available for download for subsequent use. Thus, the TrEase service offers a barrier-free entry into standard phylogenetic analyses. It is available at http://thines-lab.senckenberg.de/trease.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138529480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Fungal aromatic-bisabolane sesquiterpenoids—possible peptidylprolyl cis/trans isomerase (Pin1) inhibitors for cancer 真菌芳香双abolane倍半萜类-可能用于癌症的肽基脯氨酸顺/反式异构酶(Pin1)抑制剂

IF 2.4 3区生物学

Mycological Progress Pub Date : 2023-11-22 DOI: 10.1007/s11557-023-01934-0

Bayan E. Ainousah, Abdulrahim A. Alzain, Tagyedeen H. Shoaib, Shaimaa G. A. Mohamed, Hazem G. A. Hussein, Gamal A. Mohamed, Sabrin R. M. Ibrahim

{"title":"Fungal aromatic-bisabolane sesquiterpenoids—possible peptidylprolyl cis/trans isomerase (Pin1) inhibitors for cancer","authors":"Bayan E. Ainousah, Abdulrahim A. Alzain, Tagyedeen H. Shoaib, Shaimaa G. A. Mohamed, Hazem G. A. Hussein, Gamal A. Mohamed, Sabrin R. M. Ibrahim","doi":"10.1007/s11557-023-01934-0","DOIUrl":"https://doi.org/10.1007/s11557-023-01934-0","url":null,"abstract":"Marine fungi have been proven as potential sources of natural metabolites with significant bioactivities that have not been sufficiently explored. This highlights the need for intensifying research to reach sustainable utilization of this huge factory of biodiverse metabolites. Aromatic-bisabolane sesquiterpenoids (ABSs) are a rare class of monocyclic sesquiterpenoids that have been reported from fungi, gorgonians, corals, sponges, and plants. These metabolites possessed significant bioactivities and intriguing chemical frameworks, indicating their substantial pharmaceutical and/or agricultural values. The current work covered the reported data on fungal ABSs, including their sources, isolation, structure characterization, and bioactivities. In addition, their Pin1 inhibitory potential as anticancer agents was assessed using in silico studies. Out of the compounds studied, 17 compounds showed docking scores which surpassed that of the reference ligand. Among these, three compounds demonstrated superior MM-GBSA binding free energies compared to the reference ligand. These three compounds underwent subsequent MD simulations, confirming the stability of their interactions. These findings suggested aspergoterpenin A, engyodontiumone I, (+)-1-hydroxyboivinianic acid, and methyl(S)-3-hydroxy-4-(2-hydroxy-6-methylheptan-2-yl) benzoate as possible new Pin1 inhibitors for further in vitro against prostate and esophageal cancer cells.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138529450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multigene analyses with a broad sampling in Phytophthora and related genera provide evidence for the monophyly of downy mildews 对疫霉菌及其相关属的广泛样本进行多基因分析，为霜霉病的单系性提供了证据

IF 2.4 3区生物学

Mycological Progress Pub Date : 2023-11-17 DOI: 10.1007/s11557-023-01932-2

Marco Thines, Bagdevi Mishra, Sebastian Ploch

{"title":"Multigene analyses with a broad sampling in Phytophthora and related genera provide evidence for the monophyly of downy mildews","authors":"Marco Thines, Bagdevi Mishra, Sebastian Ploch","doi":"10.1007/s11557-023-01932-2","DOIUrl":"https://doi.org/10.1007/s11557-023-01932-2","url":null,"abstract":"Downy mildews are the most species-rich group of oomycetes, with more than 700 known species. The relationships within the main downy mildew lineages (i.e. the downy mildews with pyriform haustoria, the downy mildews with coloured conidia, and the brassicolous downy mildews) are increasingly well resolved, and 20 well-characterised monophyletic genera have been described. However, their relationships to each other, the various lineages of graminicolous downy mildews, and to the species subsumed in Phytophthora are still unresolved. Recent phylogenomic studies have suggested a polyphyly of the downy mildews, but with a limited taxon sampling within Phytophthora. As taxon sampling is crucial for inferring relationships between large groups, we have conducted a multigene analysis with a set of 72 Phytophthora species and included all known downy mildew lineages. In addition, we performed approximately unbiased (AU) testing as an additional approach to evaluate major nodes. Our analyses resolve the downy mildews as a monophyletic assemblage in all phylogenetic algorithms used. We thus conclude that the evolution of the obligate biotrophy characteristic of downy mildews was a singular event and that all downy mildew pathogens can be traced to a single ancestor.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138529454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Botryandromyces, a morphology-based genus concept scrutinized by molecular data Botryandromyces，一个基于形态学的属概念，由分子数据审查

3区生物学

Mycological Progress Pub Date : 2023-11-13 DOI: 10.1007/s11557-023-01930-4

Warre Van Caenegem, André De Kesel, Danny Haelewaters

{"title":"Botryandromyces, a morphology-based genus concept scrutinized by molecular data","authors":"Warre Van Caenegem, André De Kesel, Danny Haelewaters","doi":"10.1007/s11557-023-01930-4","DOIUrl":"https://doi.org/10.1007/s11557-023-01930-4","url":null,"abstract":"Abstract Laboulbeniales ( Ascomycota ) are an order of understudied, biotrophic microfungi uniquely associated with arthropods. More than 2300 species are described but only a fraction of those have been sequenced. Molecular studies have shown that cryptic diversity and phenotypic plasticity are present within the Laboulbeniales . Thus far, all of the 146 genera described in Laboulbeniales have been based on morphological characteristics; features commonly used to delineate genera are the organization of receptacle cells and the number of perithecial outer wall cells. The genus Botryandromyces was erected to accommodate two species, B. heteroceri and B. ornatus (type), which share similar morphological characteristics and are different from other genera in their number of perithecial outer wall cells. Here, we generated sequences of multiple loci (18S, ITS, and 28S) of B. heteroceri and several Laboulbenia species. Our phylogenetic analyses retrieved Botryandromyces within Laboulbenia with high support. The two Botryandromyces species are similar to related Laboulbenia species in their upper receptacle (i.e., cells IV and V). We propose to transfer Botryandromyces ornatus and B. heteroceri to Laboulbenia as L. heteroceri and L. mairei nom. nov., respectively, due to a complicated taxonomic history. These results advocate the use of molecular data and the necessity of an integrative taxonomy approach in the study of Laboulbeniales not only to delineate species, but also to investigate relationships among species, genera, and higher taxa as well as to understand the evolution of morphology in this group of fungi.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136348344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Clarifying the identity of marketed edible Huotanjun (Burnt Charcoal Mushroom) in southern China 澄清中国南方市售食用火炭菇的身份

3区生物学

Mycological Progress Pub Date : 2023-11-09 DOI: 10.1007/s11557-023-01927-z

Lian-hui Huang, Jing Wang, Shu-hong Li, Wei-qiang Qin, Hai-jiao Li, Xiang-hua Wang

引用次数: 0

Ecological, morphological and phylogenetic survey of Fomes fomentarius and F. inzengae (Agaricomycetes, Polyporaceae) co-occurring in the same geographic area in Central Europe 在中欧同一地理区域共生的fomentarius和F. inzengae的生态学、形态学和系统发育调查

3区生物学

Mycological Progress Pub Date : 2023-11-07 DOI: 10.1007/s11557-023-01928-y

Michal Tomšovský, Sirapitcha Kaeochulsri, Tomáš Kudláček, László Benedek Dálya

{"title":"Ecological, morphological and phylogenetic survey of Fomes fomentarius and F. inzengae (Agaricomycetes, Polyporaceae) co-occurring in the same geographic area in Central Europe","authors":"Michal Tomšovský, Sirapitcha Kaeochulsri, Tomáš Kudláček, László Benedek Dálya","doi":"10.1007/s11557-023-01928-y","DOIUrl":"https://doi.org/10.1007/s11557-023-01928-y","url":null,"abstract":"Abstract The phenomenon of cryptic species is widespread among various fungal lineages. Fomes inzengae (Ces. & De Not.) Cooke has been recently recognized as a South European kin of wood-decay basidiomycete F. fomentarius (L.) Fr. due to the problematic morphological identification of both species, their taxonomic status has been disputed. The aim of this research is to examine the distribution, host preferences, morphological characters, and phylogenetic relationships between F. fomentarius and F. inzengae in the South Moravian region in Czechia (Central Europe), where both species occur sympatrically. The results revealed the ecological preferences of Fomes spp. along an altitudinal gradient, while F. inzengae is a lowland taxon, F. fomentarius dominates at higher altitudes in forests with abundant Fagus sylvatica . The main contact zone of the two taxa is located in the upper-colline vegetation belt (elevation ca. 400‒550 m a.s.l.). The morphological analysis revealed that the basidiospore size, the width of skeletal hyphae in basidiomes, and the linear density of pores of both taxa are almost identical and can not be used for the identification of the two species. Multigene sequence analyses of ITS, LSU, RPB1, RPB2, and TEF1 markers confirmed that F. fomentarius and F. inzengae are phylogenetically distinct species. The relationship of F. inzengae and F. fomentarius to Globifomes graveolens and Hexagonia spp. is discussed.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135480531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phytophthora: an underestimated threat to agriculture, forestry, and natural ecosystems in sub-Saharan Africa 疫霉:对撒哈拉以南非洲农业、林业和自然生态系统的一种被低估的威胁

3区生物学

Mycological Progress Pub Date : 2023-10-19 DOI: 10.1007/s11557-023-01926-0

Tanay Bose, Christoffel F. J. Spies, Almuth Hammerbacher, Teresa A. Coutinho

{"title":"Phytophthora: an underestimated threat to agriculture, forestry, and natural ecosystems in sub-Saharan Africa","authors":"Tanay Bose, Christoffel F. J. Spies, Almuth Hammerbacher, Teresa A. Coutinho","doi":"10.1007/s11557-023-01926-0","DOIUrl":"https://doi.org/10.1007/s11557-023-01926-0","url":null,"abstract":"Abstract Phytophthora species are highly destructive plant pathogens and pose a significant threat to plants in various ecosystems, including agriculture, forest plantations, and natural environments. In sub-Saharan Africa, a total of 77 Phytophthora species have been identified and this review aims to provide an overview of the species diversity and progress of Phytophthora research in this region. Numerous important studies have been carried out in this region, contributing significantly to our understanding of Phytophthora in various research fields. However, compared to global data, the advancement of Phytophthora research in sub-Saharan Africa has been relatively slow. This is evident from the fact that some countries in the region have yet to report the presence of Phytophthora species. Thus, this review also highlights critical research gaps, particularly concerning the potential impacts of climate change, and suggests specific studies to address these gaps. The identified research studies are of utmost urgency as they not only aim to safeguard the iconic floral biodiversity of the region but also play a crucial role in enhancing the economy and ensuring food security.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135729853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Diverse arbuscular mycorrhizal fungi species associate with indigenous trees in a natural forest 不同的丛枝菌根真菌种类与本地树木在自然森林

3区生物学

Mycological Progress Pub Date : 2023-10-16 DOI: 10.1007/s11557-023-01922-4

Jemal yimer Kebede, Marcela Claudio Pagano, Belay Berza Beyene, Fassil Assefa Tuji

引用次数: 0

Resources and tools for studying convergent evolution in different lineages of smut fungi 研究黑穗病真菌不同谱系趋同进化的资源和工具

3区生物学

Mycological Progress Pub Date : 2023-10-13 DOI: 10.1007/s11557-023-01918-0

Lena Steins, Marine Duhamel, Sebastian Klenner-Koch, Dominik Begerow, Martin Kemler

{"title":"Resources and tools for studying convergent evolution in different lineages of smut fungi","authors":"Lena Steins, Marine Duhamel, Sebastian Klenner-Koch, Dominik Begerow, Martin Kemler","doi":"10.1007/s11557-023-01918-0","DOIUrl":"https://doi.org/10.1007/s11557-023-01918-0","url":null,"abstract":"Abstract Convergent evolution is the phenomenon of similar traits evolving independently in different lineages of the tree of life. Studying convergent evolution provides an excellent opportunity to understand natural selection for specific traits and physiological constraints to evolution that allow a broadened view on evolutionary mechanisms as a whole. Smut fungi, a polyphyletic group of plant-parasitic fungi with a specific infection and life cycle pattern, are a prime example of convergent evolution. Most notably, smut fungi in the genus Microbotryum that belongs to the subdivision Pucciniomycotina and smut fungi from the subdivision Ustilaginomycotina show strong similarities despite millions of years of independent evolution. However, the conceptual connections drawn between the two groups are scarce, thereby limiting the opportunities for exploring convergent evolution between these taxa. To facilitate knowledge exchange within the research community, we provide a summary of databases, molecular and biological tools and a brief introduction to the structure of populations and the characteristics of host specificity in both groups. Furthermore, we compare the life cycles and research emphases between the two groups. The comparisons are supplemented with an analysis of genome composition and gene function, which aims to advance research on the convergent evolution of smut fungi using existing data.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135853007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oomycete composition in Proteaceae orchards and natural stands on three continents 三大洲Proteaceae果园和天然林分的卵菌组成

3区生物学

Mycological Progress Pub Date : 2023-10-13 DOI: 10.1007/s11557-023-01925-1

Duccio Migliorini, Maria Vivas, Michael J. Wingfield, Christopher Shaw, Treena I. Burgess

{"title":"Oomycete composition in Proteaceae orchards and natural stands on three continents","authors":"Duccio Migliorini, Maria Vivas, Michael J. Wingfield, Christopher Shaw, Treena I. Burgess","doi":"10.1007/s11557-023-01925-1","DOIUrl":"https://doi.org/10.1007/s11557-023-01925-1","url":null,"abstract":"Abstract The Proteaceae , a diverse family of woody flowering plants in the Southern Hemisphere, contains many species known to be susceptible to Phytophthora cinnamomi , both in the natural environment and in cut-flower orchards. Very little is known about the prevalence of P. cinnamomi and other oomycetes across these landscapes. To address this knowledge gap, we used a double ITS1 and RPS10 gene metabarcoding approach and traditional isolation protocols to investigate oomycetes in orchards and natural stands of Proteaceae across South Africa, South Africa (eastern and western), Australia, and Europe. The RPS10 primers amplified more samples, including various Pythium species, while the ITS primers detected more Phytophthora phylotypes. Both datasets showed that geographic regions influenced oomycete species richness and community composition, while they did not show any variation between orchards and natural vegetation. RPS10 metabarcoding detected the largest number of species and provided greater statistical confidence than ITS1 when considering oomycete species composition. Metabarcoding also showed that orchards had a higher abundance of P. cinnamomi compared to native stands, although this was not found when isolating through baiting of roots and rhizosphere soil. Direct isolation and metabarcoding are complementary, with metabarcoding serving as an early detection tool. However, it cannot distinguish living viable propagules from residual DNA of dead propagules, limiting its use for diagnostic purposes related to Phytophthora management and control. These results, along with those of other recent studies, show that metabarcoding offers an effective tool to describe the dynamics of soil oomycetes in different ecosystems.","PeriodicalId":19111,"journal":{"name":"Mycological Progress","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135854085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0