Pub Date : 2023-07-06DOI: 10.1186/s43008-023-00118-5
Yong-Jie Zhang, Xiang-Ping Fan, Jia-Ni Li, Shu Zhang
Cordyceps is a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome of Cordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, including cob (1 intron), cox1 (4), cox3 (3), nad1 (1), nad4 (1), nad5 (1), and rnl (3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five different Cordyceps species (i.e., C. blackwelliae, C. chanhua, C. militaris, C. pruinosa, and C. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. This study promotes our understanding of fungal evolution in Cordyceps.
{"title":"Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps.","authors":"Yong-Jie Zhang, Xiang-Ping Fan, Jia-Ni Li, Shu Zhang","doi":"10.1186/s43008-023-00118-5","DOIUrl":"https://doi.org/10.1186/s43008-023-00118-5","url":null,"abstract":"<p><p>Cordyceps is a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome of Cordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, including cob (1 intron), cox1 (4), cox3 (3), nad1 (1), nad4 (1), nad5 (1), and rnl (3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five different Cordyceps species (i.e., C. blackwelliae, C. chanhua, C. militaris, C. pruinosa, and C. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. This study promotes our understanding of fungal evolution in Cordyceps.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"13"},"PeriodicalIF":5.4,"publicationDate":"2023-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10327131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9802467","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 : 2023-06-28DOI: 10.1186/s43008-023-00117-6
Yoonhee Cho, Dohye Kim, Yoongil Lee, Juhwan Jeong, Shahid Hussain, Young Woon Lim
Although there is a continuous increase in available molecular data, not all sequence identities in public databases are always properly verified and managed. Here, the sequences available in GenBank for Fuscoporia (Hymenochaetales) were validated. Many morphological characters of Fuscoporia overlap among the species, emphasizing the role of molecular identification for accuracy. The identities of 658 Fuscoporia GenBank internal transcribed spacer (ITS) sequences were assessed using ITS phylogeny, revealing 109 (16.6%) misidentified and 196 (29.8%) unspecified sequences. They were validated and re-identified based on the research articles they were published in and, if unpublished, based on sequences from the type, type locality-derived sequences, or otherwise reliable sequences. To enhance the resolution of species delimitation, a phylogenetic assessment of a multi-marker dataset (ITS + nrLSU + rpb2 + tef1) was conducted. The multi-marker phylogeny resolved five of the twelve species complexes found in the ITS phylogeny and uncovered five new Fuscoporia species: F. dolichoseta, F. gilvoides, F. koreana, F. reticulata, and F. semicephala. The validated ITS sequences in this study may prevent further accumulation of misidentified sequences in public databases and contribute to a more accurate taxonomic evaluation of Fuscoporia species.
{"title":"Validation of Fuscoporia (Hymenochaetales, Basidiomycota) ITS sequences and five new species based on multi-marker phylogenetic and morphological analyses.","authors":"Yoonhee Cho, Dohye Kim, Yoongil Lee, Juhwan Jeong, Shahid Hussain, Young Woon Lim","doi":"10.1186/s43008-023-00117-6","DOIUrl":"https://doi.org/10.1186/s43008-023-00117-6","url":null,"abstract":"<p><p>Although there is a continuous increase in available molecular data, not all sequence identities in public databases are always properly verified and managed. Here, the sequences available in GenBank for Fuscoporia (Hymenochaetales) were validated. Many morphological characters of Fuscoporia overlap among the species, emphasizing the role of molecular identification for accuracy. The identities of 658 Fuscoporia GenBank internal transcribed spacer (ITS) sequences were assessed using ITS phylogeny, revealing 109 (16.6%) misidentified and 196 (29.8%) unspecified sequences. They were validated and re-identified based on the research articles they were published in and, if unpublished, based on sequences from the type, type locality-derived sequences, or otherwise reliable sequences. To enhance the resolution of species delimitation, a phylogenetic assessment of a multi-marker dataset (ITS + nrLSU + rpb2 + tef1) was conducted. The multi-marker phylogeny resolved five of the twelve species complexes found in the ITS phylogeny and uncovered five new Fuscoporia species: F. dolichoseta, F. gilvoides, F. koreana, F. reticulata, and F. semicephala. The validated ITS sequences in this study may prevent further accumulation of misidentified sequences in public databases and contribute to a more accurate taxonomic evaluation of Fuscoporia species.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"12"},"PeriodicalIF":5.4,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10308793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9784043","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 : 2023-06-06DOI: 10.1186/s43008-023-00116-7
Shan Shen, Shi-Liang Liu, Li-Wei Zhou
The genus is a special and crucial taxonomic rank compared with others above the species level, because a species has to be placed in a certain genus instead of any other higher ranks. With more and more new species being described, the placements of their generic position are sometimes incorrect due to the simple phylogenies resulting from inappropriate sampling. Here, we focus on the taxonomy of a small wood-inhabiting fungal genus Hyphodermella. With the most comprehensive sampling to date, the phylogenetic position of Hyphodermella within Phanerochaetaceae is rearranged by employing the same ITS and nLSU regions as in previous studies and also the ITS, nLSU, rpb1, rpb2 and tef1α regions. Three species are excluded from Hyphodermella: H. poroides is placed in a newly introduced monotypic genus Pseudohyphodermella, while H. aurantiaca and H. zixishanensis are transferred to Roseograndinia. Hyphodermella suiae is described as a new species from South China and Vietnam. Keys to eight species in Hyphodermella and five in Roseograndinia are provided. Beyond solving the taxonomic issue of Hyphodermella itself, the current study also aims to suggest that all fungal taxonomists especially beginners should keep in mind to sample as many comprehensive taxa as possible in phylogenetic analyses.
{"title":"Taxonomy of Hyphodermella: a case study to show that simple phylogenies cannot always accurately place species in appropriate genera.","authors":"Shan Shen, Shi-Liang Liu, Li-Wei Zhou","doi":"10.1186/s43008-023-00116-7","DOIUrl":"10.1186/s43008-023-00116-7","url":null,"abstract":"<p><p>The genus is a special and crucial taxonomic rank compared with others above the species level, because a species has to be placed in a certain genus instead of any other higher ranks. With more and more new species being described, the placements of their generic position are sometimes incorrect due to the simple phylogenies resulting from inappropriate sampling. Here, we focus on the taxonomy of a small wood-inhabiting fungal genus Hyphodermella. With the most comprehensive sampling to date, the phylogenetic position of Hyphodermella within Phanerochaetaceae is rearranged by employing the same ITS and nLSU regions as in previous studies and also the ITS, nLSU, rpb1, rpb2 and tef1α regions. Three species are excluded from Hyphodermella: H. poroides is placed in a newly introduced monotypic genus Pseudohyphodermella, while H. aurantiaca and H. zixishanensis are transferred to Roseograndinia. Hyphodermella suiae is described as a new species from South China and Vietnam. Keys to eight species in Hyphodermella and five in Roseograndinia are provided. Beyond solving the taxonomic issue of Hyphodermella itself, the current study also aims to suggest that all fungal taxonomists especially beginners should keep in mind to sample as many comprehensive taxa as possible in phylogenetic analyses.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"11"},"PeriodicalIF":5.2,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9954000","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 : 2023-05-11DOI: 10.1186/s43008-023-00114-9
Dexiang Tang, Ou Huang, Weiqiu Zou, Yuanbing Wang, Yao Wang, Quanying Dong, Tao Sun, Gang Yang, Hong Yu
Some Ophiocordyceps species infecting ants are able to manipulate the host behavior. The hosts are manipulated in order to move to location that are advantageous for fungal spore transmission. Ophiocordyceps species that are able to manipulate the ant's behavior are called "zombie-ant fungi". They are widespread within tropical forests worldwide, with relatively few reports from subtropical monsoon evergreen broad-leaf forest. Zombie-ant fungi have been described and reported in different countries worldwide. However, there were a few reports from China. This study proposed six new species of zombie-ant fungi from China based on multi-gene (SSU, LSU, TEF, RPB1 and RPB2) phylogenetic analyses and morphological characteristics. Six novel species of Ophiocordyceps from China were identified as the Ophiocordyceps unilateralis core clade, forming a separate lineage with other species. Six novel species of Ophiocordyceps with hirsutella-like asexual morphs exclusively infecting ants were presented herein, namely, Ophiocordyceps acroasca, Ophiocordyceps bifertilis, Ophiocordyceps subtiliphialida, Ophiocordyceps basiasca, Ophiocordyceps nuozhaduensis and Ophiocordyceps contiispora. Descriptions and illustrations for six taxon were provided. Five of these species were collected from the subtropical monsoon evergreen broad-leaf forest, and one was collected from the rainforest and subtropical monsoon evergreen broad-leaf forest. This work proposes that the same host of Camponotus can be infected by multiple ant pathogenic fungi, while multiple ants of Polyrhachis can be infected by the same pathogenic fungi at the same time. This study contributes towards a better understanding of the evolutionary relationship between hosts and fungi, and provides novel insights into the morphology, distribution, parasitism, and ecology of Ophiocordyceps unilateralis sensu lato. We have provided a method for obtaining living cultures of Ophiocordyceps unilateralis complex species and their asexual morphs based on the living cultures, which is of significant value for further studies of Ophiocordyceps unilateralis complex species in the future.
{"title":"Six new species of zombie-ant fungi from Yunnan in China.","authors":"Dexiang Tang, Ou Huang, Weiqiu Zou, Yuanbing Wang, Yao Wang, Quanying Dong, Tao Sun, Gang Yang, Hong Yu","doi":"10.1186/s43008-023-00114-9","DOIUrl":"10.1186/s43008-023-00114-9","url":null,"abstract":"<p><p>Some Ophiocordyceps species infecting ants are able to manipulate the host behavior. The hosts are manipulated in order to move to location that are advantageous for fungal spore transmission. Ophiocordyceps species that are able to manipulate the ant's behavior are called \"zombie-ant fungi\". They are widespread within tropical forests worldwide, with relatively few reports from subtropical monsoon evergreen broad-leaf forest. Zombie-ant fungi have been described and reported in different countries worldwide. However, there were a few reports from China. This study proposed six new species of zombie-ant fungi from China based on multi-gene (SSU, LSU, TEF, RPB1 and RPB2) phylogenetic analyses and morphological characteristics. Six novel species of Ophiocordyceps from China were identified as the Ophiocordyceps unilateralis core clade, forming a separate lineage with other species. Six novel species of Ophiocordyceps with hirsutella-like asexual morphs exclusively infecting ants were presented herein, namely, Ophiocordyceps acroasca, Ophiocordyceps bifertilis, Ophiocordyceps subtiliphialida, Ophiocordyceps basiasca, Ophiocordyceps nuozhaduensis and Ophiocordyceps contiispora. Descriptions and illustrations for six taxon were provided. Five of these species were collected from the subtropical monsoon evergreen broad-leaf forest, and one was collected from the rainforest and subtropical monsoon evergreen broad-leaf forest. This work proposes that the same host of Camponotus can be infected by multiple ant pathogenic fungi, while multiple ants of Polyrhachis can be infected by the same pathogenic fungi at the same time. This study contributes towards a better understanding of the evolutionary relationship between hosts and fungi, and provides novel insights into the morphology, distribution, parasitism, and ecology of Ophiocordyceps unilateralis sensu lato. We have provided a method for obtaining living cultures of Ophiocordyceps unilateralis complex species and their asexual morphs based on the living cultures, which is of significant value for further studies of Ophiocordyceps unilateralis complex species in the future.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"9"},"PeriodicalIF":5.2,"publicationDate":"2023-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10173673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9806952","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 : 2023-05-11DOI: 10.1186/s43008-023-00115-8
Maryam Rafiqi, Chatchai Kosawang, Jessica A Peers, Lukas Jelonek, Hélène Yvanne, Mark McMullan, Lene R Nielsen
Tree diseases constitute a significant threat to biodiversity worldwide. Pathogen discovery in natural habitats is of vital importance to understanding current and future threats and prioritising efforts towards developing disease management strategies. Ash dieback is a fungal disease of major conservational concern that is infecting common ash trees, Fraxinus excelsior, in Europe. The disease is caused by a non-native fungal pathogen, Hymenoscyphus fraxineus. Other dieback causing-species have not previously been identified in the genus Hymenoscyphus. Here, we discover the pathogenicity potential of two newly identified related species of Asian origin, H. koreanus and H. occultus, and one Europe-native related species, H. albidus. We sequence the genomes of all three Hymenoscyphus species and compare them to that of H. fraxineus. Phylogenetic analysis of core eukaryotic genes identified H. albidus and H. koreanus as sister species, whilst H. occultus diverged prior to these and H. fraxineus. All four Hymenoscyphus genomes are of comparable size (55-62 Mbp) and GC contents (42-44%) and encode for polymorphic secretomes. Surprisingly, 1133 predicted secreted proteins are shared between the ash dieback pathogen H. fraxineus and the three related Hymenoscyphus endophytes. Amongst shared secreted proteins are cell death-inducing effector candidates, such as necrosis, and ethylene-inducing peptide 1-like proteins, Nep1-like proteins, that are upregulated during in planta growth of all Hymenoscyphus species. Indeed, pathogenicity tests showed that all four related Hymenoscyphus species develop pathogenic growth on European ash stems, with native H. albidus being the least virulent. Our results identify the threat Hymenoscypohus species pose to the survival of European ash trees, and highlight the importance of promoting pathogen surveillance in environmental landscapes. Identifying new pathogens and including them in the screening for durable immunity of common ash trees is key to the long-term survival of ash in Europe.
树木病害对全球生物多样性构成重大威胁。在自然栖息地发现病原体对于了解当前和未来的威胁以及优先制定疾病管理策略至关重要。白蜡树枯死病是一种真菌疾病,是欧洲常见的白蜡树(Fraxinus excelsior)感染的主要保护性疾病。这种病是由一种非本地真菌病原体--Hymenoscyphus fraxineus 引起的。在 Hymenoscyphus 属中,以前尚未发现其他导致枯死的物种。在这里,我们发现了两个新发现的亚洲相关物种 H. koreanus 和 H. occultus 以及一个欧洲本地相关物种 H. albidus 的致病潜力。我们对所有三个Hymenoscyphus物种的基因组进行了测序,并与H. fraxineus的基因组进行了比较。通过对核心真核基因的系统进化分析,我们发现 H. albidus 和 H. koreanus 是姊妹种,而 H. occultus 比它们和 H. fraxineus 早分化。所有四个Hymenoscyphus基因组的大小(55-62 Mbp)和GC含量(42-44%)相当,并编码多态分泌物。令人惊讶的是,白蜡枯病原体 H. fraxineus 和三种相关的 Hymenoscyphus 内生菌之间共有 1133 个预测分泌蛋白。在共享的分泌蛋白中,有诱导细胞死亡的效应物候选蛋白,如坏死蛋白和乙烯诱导肽 1 样蛋白、Nep1 样蛋白,这些蛋白在所有 Hymenoscyphus 物种的植物生长过程中都会上调。事实上,致病性测试表明,所有四种相关的白蜡姬松柏属(Hymenoscyphus)都会在欧洲白蜡茎上生长致病,而本地的白蜡姬松柏属(H. albidus)毒性最低。我们的研究结果确定了白蜡树种对欧洲白蜡树的生存构成的威胁,并强调了在环境景观中促进病原体监测的重要性。识别新病原体并将其纳入普通白蜡树持久免疫力的筛选中,是欧洲白蜡树长期生存的关键。
{"title":"Endophytic fungi related to the ash dieback causal agent encode signatures of pathogenicity on European ash.","authors":"Maryam Rafiqi, Chatchai Kosawang, Jessica A Peers, Lukas Jelonek, Hélène Yvanne, Mark McMullan, Lene R Nielsen","doi":"10.1186/s43008-023-00115-8","DOIUrl":"10.1186/s43008-023-00115-8","url":null,"abstract":"<p><p>Tree diseases constitute a significant threat to biodiversity worldwide. Pathogen discovery in natural habitats is of vital importance to understanding current and future threats and prioritising efforts towards developing disease management strategies. Ash dieback is a fungal disease of major conservational concern that is infecting common ash trees, Fraxinus excelsior, in Europe. The disease is caused by a non-native fungal pathogen, Hymenoscyphus fraxineus. Other dieback causing-species have not previously been identified in the genus Hymenoscyphus. Here, we discover the pathogenicity potential of two newly identified related species of Asian origin, H. koreanus and H. occultus, and one Europe-native related species, H. albidus. We sequence the genomes of all three Hymenoscyphus species and compare them to that of H. fraxineus. Phylogenetic analysis of core eukaryotic genes identified H. albidus and H. koreanus as sister species, whilst H. occultus diverged prior to these and H. fraxineus. All four Hymenoscyphus genomes are of comparable size (55-62 Mbp) and GC contents (42-44%) and encode for polymorphic secretomes. Surprisingly, 1133 predicted secreted proteins are shared between the ash dieback pathogen H. fraxineus and the three related Hymenoscyphus endophytes. Amongst shared secreted proteins are cell death-inducing effector candidates, such as necrosis, and ethylene-inducing peptide 1-like proteins, Nep1-like proteins, that are upregulated during in planta growth of all Hymenoscyphus species. Indeed, pathogenicity tests showed that all four related Hymenoscyphus species develop pathogenic growth on European ash stems, with native H. albidus being the least virulent. Our results identify the threat Hymenoscypohus species pose to the survival of European ash trees, and highlight the importance of promoting pathogen surveillance in environmental landscapes. Identifying new pathogens and including them in the screening for durable immunity of common ash trees is key to the long-term survival of ash in Europe.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"10"},"PeriodicalIF":5.2,"publicationDate":"2023-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10176688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9828700","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 : 2023-04-07DOI: 10.1186/s43008-023-00111-y
Rhudson Henrique Santos Ferreira da Cruz, Jefferson Dos Santos Góis, Paulo Marinho, Iuri Goulart Baseia, Kentaro Hosaka
The genus Cyathus was established in 1768, but more in-depth taxonomic studies with the group only occurred after 1844. In the following years, changes in the infrageneric classification of Cyathus were proposed based mainly on morphology. With advances in phylogenetic studies, the morphological classifications were tested and a new subdivision into three groups was proposed in 2007. Based on the last two classifications, this work aims to expand and understand the internal phylogenetic relationships among the fungi of the genus Cyathus and examine how these relationships are reflected in the taxonomic classification, through molecular analyses covering most of the species in the group, based on materials obtained from type specimens deposited in major fungal collections worldwide, besides expanding sampling with tropical species. Molecular analyses followed the protocols available in the literature, including the design of specific primers for Cyathus. In the phylogenetic analysis, using Maximum Parsimony and Bayesian methods, sequences of ITS and LSU regions from 41 samples of 39 species of Cyathus, 26 were placed with some nomenclatural types. The monophyly of Cyathus was confirmed with maximum support in both tests, and the infrageneric groups of the most recent classification were unchanged, but the clade striatum showed segregation into four groups and three subgroups. The phylogenetic organization is supported morphological characters, and diagnoses are presented for each group, as well as a dichotomous key for the infrageneric separation.
{"title":"Rearranging the Bird's Nest Fungi: molecular review of internal clades in Cyathus (Nidulariaceae, Basidiomycota).","authors":"Rhudson Henrique Santos Ferreira da Cruz, Jefferson Dos Santos Góis, Paulo Marinho, Iuri Goulart Baseia, Kentaro Hosaka","doi":"10.1186/s43008-023-00111-y","DOIUrl":"https://doi.org/10.1186/s43008-023-00111-y","url":null,"abstract":"<p><p>The genus Cyathus was established in 1768, but more in-depth taxonomic studies with the group only occurred after 1844. In the following years, changes in the infrageneric classification of Cyathus were proposed based mainly on morphology. With advances in phylogenetic studies, the morphological classifications were tested and a new subdivision into three groups was proposed in 2007. Based on the last two classifications, this work aims to expand and understand the internal phylogenetic relationships among the fungi of the genus Cyathus and examine how these relationships are reflected in the taxonomic classification, through molecular analyses covering most of the species in the group, based on materials obtained from type specimens deposited in major fungal collections worldwide, besides expanding sampling with tropical species. Molecular analyses followed the protocols available in the literature, including the design of specific primers for Cyathus. In the phylogenetic analysis, using Maximum Parsimony and Bayesian methods, sequences of ITS and LSU regions from 41 samples of 39 species of Cyathus, 26 were placed with some nomenclatural types. The monophyly of Cyathus was confirmed with maximum support in both tests, and the infrageneric groups of the most recent classification were unchanged, but the clade striatum showed segregation into four groups and three subgroups. The phylogenetic organization is supported morphological characters, and diagnoses are presented for each group, as well as a dichotomous key for the infrageneric separation.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"8"},"PeriodicalIF":5.4,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10082518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9257612","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}
Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.
{"title":"The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales.","authors":"Qiang Li, Wenqi Xiao, Peng Wu, Ting Zhang, Peng Xiang, Qian Wu, Liang Zou, Mingying Gui","doi":"10.1186/s43008-023-00112-x","DOIUrl":"https://doi.org/10.1186/s43008-023-00112-x","url":null,"abstract":"<p><p>Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"7"},"PeriodicalIF":5.4,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10064765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9245809","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 : 2023-03-30DOI: 10.1186/s43008-023-00113-w
Samad Ashrafi, Jan-Peer Wennrich, Yvonne Becker, Jose G Maciá-Vicente, Anke Brißke-Rode, Matthias Daub, Torsten Thünen, Abdelfattah A Dababat, Maria R Finckh, Marc Stadler, Wolfgang Maier
In this study fungal strains were investigated, which had been isolated from eggs of the cereal cyst nematode Heterodera filipjevi, and roots of Microthlaspi perfoliatum (Brassicaceae). The morphology, the interaction with nematodes and plants and the phylogenetic relationships of these strains originating from a broad geographic range covering Western Europe to Asia Minor were studied. Phylogenetic analyses using five genomic loci including ITSrDNA, LSUrDNA, SSUrDNA, rpb2 and tef1-α were carried out. The strains were found to represent a distinct phylogenetic lineage most closely related to Equiseticola and Ophiosphaerella, and Polydomus karssenii (Phaeosphaeriaceae, Pleosporales) is introduced here as a new species representing a monotypic genus. The pathogenicity tests against nematode eggs fulfilled Koch's postulates using in vitro nematode bioassays and showed that the fungus could parasitise its original nematode host H. filipjevi as well as the sugar beet cyst nematode H. schachtii, and colonise cysts and eggs of its hosts by forming highly melanised moniliform hyphae. Light microscopic observations on fungus-root interactions in an axenic system revealed the capacity of the same fungal strain to colonise the roots of wheat and produce melanised hyphae and microsclerotia-like structure typical for dark septate endophytes. Confocal laser scanning microscopy further demonstrated that the fungus colonised the root cells by predominant intercellular growth of hyphae, and frequent formation of appressorium-like as well as penetration peg-like structures through internal cell walls surrounded by callosic papilla-like structures. Different strains of the new fungus produced a nearly identical set of secondary metabolites with various biological activities including nematicidal effects irrespective of their origin from plants or nematodes.
{"title":"Polydomus karssenii gen. nov. sp. nov. is a dark septate endophyte with a bifunctional lifestyle parasitising eggs of plant parasitic cyst nematodes (Heterodera spp.).","authors":"Samad Ashrafi, Jan-Peer Wennrich, Yvonne Becker, Jose G Maciá-Vicente, Anke Brißke-Rode, Matthias Daub, Torsten Thünen, Abdelfattah A Dababat, Maria R Finckh, Marc Stadler, Wolfgang Maier","doi":"10.1186/s43008-023-00113-w","DOIUrl":"https://doi.org/10.1186/s43008-023-00113-w","url":null,"abstract":"<p><p>In this study fungal strains were investigated, which had been isolated from eggs of the cereal cyst nematode Heterodera filipjevi, and roots of Microthlaspi perfoliatum (Brassicaceae). The morphology, the interaction with nematodes and plants and the phylogenetic relationships of these strains originating from a broad geographic range covering Western Europe to Asia Minor were studied. Phylogenetic analyses using five genomic loci including ITSrDNA, LSUrDNA, SSUrDNA, rpb2 and tef1-α were carried out. The strains were found to represent a distinct phylogenetic lineage most closely related to Equiseticola and Ophiosphaerella, and Polydomus karssenii (Phaeosphaeriaceae, Pleosporales) is introduced here as a new species representing a monotypic genus. The pathogenicity tests against nematode eggs fulfilled Koch's postulates using in vitro nematode bioassays and showed that the fungus could parasitise its original nematode host H. filipjevi as well as the sugar beet cyst nematode H. schachtii, and colonise cysts and eggs of its hosts by forming highly melanised moniliform hyphae. Light microscopic observations on fungus-root interactions in an axenic system revealed the capacity of the same fungal strain to colonise the roots of wheat and produce melanised hyphae and microsclerotia-like structure typical for dark septate endophytes. Confocal laser scanning microscopy further demonstrated that the fungus colonised the root cells by predominant intercellular growth of hyphae, and frequent formation of appressorium-like as well as penetration peg-like structures through internal cell walls surrounded by callosic papilla-like structures. Different strains of the new fungus produced a nearly identical set of secondary metabolites with various biological activities including nematicidal effects irrespective of their origin from plants or nematodes.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"6"},"PeriodicalIF":5.4,"publicationDate":"2023-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10064538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9602868","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 : 2023-03-07DOI: 10.1186/s43008-023-00110-z
Wei-Lin Mao, Ying-Da Wu, Hong-Gao Liu, Yuan Yuan, Yu-Cheng Dai
The polypores with shallow pores from tropical Asia and America are studied. Our molecular phylogeny based on the internal transcribed spacer (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), the translation elongation factor 1-α gene (TEF1), and the largest subunit of RNA polymerase II (RPB1) demonstrates six clades are formed among Porogramme and related genera. Two new genera, Cyanoporus and Pseudogrammothele, are established, and the six clades represent Porogramme, Cyanoporus, Grammothele, Epithele, Theleporus, and Pseudogrammothele, respectively. The molecular clock analyses estimate the divergence times of the six clades based on a dataset (ITS + LSU + TEF1 + RPB1 + RPB2), and we recognize the mean stem ages of the six genera are earlier than 50 Mya. Three new species in Porogramme were morphologically and phylogenetically confirmed, and they are described as P. austroasiana, P. cylindrica, and P. yunnanensis. Phylogenetic analysis shows that type species of Tinctoporellus and Porogramme are nested in the same clade, and Tinctoporellus is treated as a synonym of Porogramme. Based on our phylogeny, twelve new combinations are proposed, and the differences between the new species and similar or related species are discussed.
{"title":"A contribution to Porogramme (Polyporaceae, Agaricomycetes) and related genera.","authors":"Wei-Lin Mao, Ying-Da Wu, Hong-Gao Liu, Yuan Yuan, Yu-Cheng Dai","doi":"10.1186/s43008-023-00110-z","DOIUrl":"https://doi.org/10.1186/s43008-023-00110-z","url":null,"abstract":"<p><p>The polypores with shallow pores from tropical Asia and America are studied. Our molecular phylogeny based on the internal transcribed spacer (ITS), the large subunit nuclear ribosomal RNA gene (nLSU), the translation elongation factor 1-α gene (TEF1), and the largest subunit of RNA polymerase II (RPB1) demonstrates six clades are formed among Porogramme and related genera. Two new genera, Cyanoporus and Pseudogrammothele, are established, and the six clades represent Porogramme, Cyanoporus, Grammothele, Epithele, Theleporus, and Pseudogrammothele, respectively. The molecular clock analyses estimate the divergence times of the six clades based on a dataset (ITS + LSU + TEF1 + RPB1 + RPB2), and we recognize the mean stem ages of the six genera are earlier than 50 Mya. Three new species in Porogramme were morphologically and phylogenetically confirmed, and they are described as P. austroasiana, P. cylindrica, and P. yunnanensis. Phylogenetic analysis shows that type species of Tinctoporellus and Porogramme are nested in the same clade, and Tinctoporellus is treated as a synonym of Porogramme. Based on our phylogeny, twelve new combinations are proposed, and the differences between the new species and similar or related species are discussed.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"5"},"PeriodicalIF":5.4,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9990255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9089487","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 : 2023-02-23DOI: 10.1186/s43008-023-00109-6
Martin S Mullett, Kris Van Poucke, Annelies Haegeman, Fran Focquet, Nicholas C Cauldron, Brian J Knaus, Marilia Horta Jung, Koji Kageyama, Ayaka Hieno, Hayato Masuja, Seiji Uematsu, Joan F Webber, Clive M Brasier, József Bakonyi, Kurt Heungens, Niklaus J Grünwald, Thomas Jung
Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples (Malus), oaks (Quercus), and beech (Fagus). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts (Castanea, Quercus, Fagus). Isolates from fruit trees (Prunus and Malus) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora, which may potentially be a separate sister species and has likely been moved with live plants. The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity.
外来入侵植物病原体对本地和农业生态系统构成重大威胁。疫霉(Phytophthora x cambivora)是森林和果树的一种入侵性、破坏性病原体,在世界范围内对栗子(Castanea)、杏、桃、李、杏仁和樱桃(Prunus)、苹果(Malus)、橡树(Quercus)和山毛榉(Fagus)造成严重危害。它是最早被引入欧洲和北美的具有破坏性的入侵疫霉物种之一,尽管它的起源尚不清楚。我们利用基因分型测序技术确定了其在欧洲、北美和南美、澳大利亚和东亚(主要是日本)的种群遗传史。欧洲和澳大利亚的种群表现为无性繁殖,北美的种群表现为高度无性繁殖,但有一定程度的有性繁殖,东亚的种群表现为部分有性繁殖。两个交配类型相反的无性系和一个由这两个无性系衍生的杂交系在欧洲的种群中占主导地位,并主要发现于壳状森林寄主(Castanea, Quercus, Fagus)上。在澳大利亚、北美、欧洲和东亚发现的果树(李子和苹果)分离株属于一个单独的谱系,这表明果树上的疾病可能是由P. x cambivora的一个独特谱系引起的,它可能是一个单独的姐妹物种,可能是随着活植物移动的。在日本发现了最高的遗传多样性,这表明东亚是病原体的起源中心。需要在东亚未取样的温带地区进行进一步调查,以便更精确地确定多样性中心的位置和范围。
{"title":"Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora.","authors":"Martin S Mullett, Kris Van Poucke, Annelies Haegeman, Fran Focquet, Nicholas C Cauldron, Brian J Knaus, Marilia Horta Jung, Koji Kageyama, Ayaka Hieno, Hayato Masuja, Seiji Uematsu, Joan F Webber, Clive M Brasier, József Bakonyi, Kurt Heungens, Niklaus J Grünwald, Thomas Jung","doi":"10.1186/s43008-023-00109-6","DOIUrl":"https://doi.org/10.1186/s43008-023-00109-6","url":null,"abstract":"<p><p>Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples (Malus), oaks (Quercus), and beech (Fagus). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts (Castanea, Quercus, Fagus). Isolates from fruit trees (Prunus and Malus) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora, which may potentially be a separate sister species and has likely been moved with live plants. The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity.</p>","PeriodicalId":54345,"journal":{"name":"Ima Fungus","volume":"14 1","pages":"4"},"PeriodicalIF":5.4,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9951538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9349158","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}