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Nie Y, Yin Y, Zhao H, Liu X, Huang B. Unveiling species diversity within the family Conidiobolaceae (Entomophthorales) in China: Descriptions of two new species and reassessment of the taxonomic position of Conidioboluspolyspermus. MycoKeys 2024; 105:203-216. [PMID: 38818111 PMCID: PMC11137373 DOI: 10.3897/mycokeys.105.117871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
In the present study, two new Conidiobolus s.s. species were described relying on the morphological studies and phylogenetic analysis utilizing nuclear large subunit of rDNA (nucLSU), mitochondrial small subunit of rDNA (mtSSU), and elongation-factor-like gene (EFL) sequences. Conidiobolusjiangxiensissp. nov. is distinguished by its short primary conidiophores, a feature not commonly observed in other Conidiobolus s.s. species. Conversely, Conidiobolusmarcoconidiussp. nov. is characterized by larger primary conidia and the emergence of 2-5 secondary conidia from each branched secondary conidiophores. Additionally, the taxonomic reassessment of C.polyspermus confirms its distinct status within the genus Conidiobolus s.s. Moreover, molecular analyses, incorporating the nucLSU, mtSSU, and EFL sequences, provide robust support for the phylogenetic placement of the two newly described species and the taxonomic identity of C.polyspermus. This investigation contributes valuable insights into the species diversity of Conidiobolaceae in China, enhancing our understanding of the taxonomy within this fungal family.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, ChinaAnhui University of TechnologyHefeiChina
| | - Ying Yin
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui Agricultural UniversityHefeiChina
| | - Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - XiaoYong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, ChinaShandong Normal UniversityJinanChina
| | - Bo Huang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui Agricultural UniversityHefeiChina
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2
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. eLife 2024; 12:RP92863. [PMID: 38767950 PMCID: PMC11105155 DOI: 10.7554/elife.92863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-RiversideRiversideUnited States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARSIthacaUnited States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angie M Macias
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Ann E Hajek
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Benjamin L de Bivort
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Matt T Kasson
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagenDenmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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3
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Lu H, Nie Y, Huang B. The second complete mitochondrial genome of Capillidium rhysosporum within the family Capillidiaceae, Entomophthorales. Mitochondrial DNA B Resour 2024; 9:332-337. [PMID: 38476836 PMCID: PMC10930110 DOI: 10.1080/23802359.2024.2324938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The complete mitochondrial genome of the entomophthoroid fungus Capillidium rhysosporum (strain no.: ATCC 12588) was sequenced using next-generation sequencing technology. The assembled circular genome has a length of 46,756 base pairs with a GC content of 27.06%. Gene prediction identified 15 core protein-coding genes (PCGs), two rRNA genes, and 27 tRNA genes. Phylogenetic analysis confirmed that C. rhysosporum belongs to the Zoopagomycota clade and is closely related to C. heterosporum. This study presents the second complete mitochondrial genome within the family Capillidiaceae, contributing to the mitochondrial DNA database of entomophthoroid fungi.
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Affiliation(s)
- Hanwen Lu
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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4
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.13.557621. [PMID: 37745330 PMCID: PMC10515909 DOI: 10.1101/2023.09.13.557621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA United States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY, United States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Angie M. Macias
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Ann E. Hajek
- Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Benjamin L. de Bivort
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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5
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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6
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Nie Y, Cai Y, Zhao H, Zhou Z, Zhao C, Liu X, Huang B. Morphological and phylogenetic analyses reveal two new species in Conidiobolus s.s. (Conidiobolaceae, Entomophthorales) from China. MycoKeys 2023; 98:221-232. [PMID: 37456576 PMCID: PMC10339111 DOI: 10.3897/mycokeys.98.103603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023] Open
Abstract
The genus Conidiobolus s.s. (Conidiobolaceae, Entomophthorales) has been delimited to accommodate members that produce microspores. Herein, morphological studies, combined with phylogenetic analysis based on the nuclear large subunit of rDNA (nucLSU), the mitochondrial small subunit of rDNA (mtSSU), and the elongation-factor-like gene (EFL) revealed two Conidiobolus s.s. species isolated from plant debris in China. Conidioboluslongiconidiophorussp. nov. is mainly characterised by its long primary conidiophores, while Conidioboluspolysporussp. nov. is diagnosed by 2-3 primary conidia arising from branched primary conidiophores. Phylogenetically, the former is grouped into a separate clade, while the latter is closely related to C.incongruus, but is morphologically distinguished by its larger primary conidia and branched conidiophores.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, ChinaAnhui Agricultural UniversityHefeiChina
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan 243002, ChinaAnhui University of TechnologyMa'anshanChina
| | - Yue Cai
- Department of Biological and Environmental Engineering, Hefei University, Hefei 230601, ChinaHefei UniversityHefeiChina
| | - Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - ZhengYu Zhou
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan 243002, ChinaAnhui University of TechnologyMa'anshanChina
| | - ChangWei Zhao
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan 243002, ChinaAnhui University of TechnologyMa'anshanChina
| | - XiaoYong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, ChinaShandong Normal UniversityJinanChina
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, ChinaAnhui Agricultural UniversityHefeiChina
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7
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Sacco NE, Hajek AE. Diversity and Breadth of Host Specificity among Arthropod Pathogens in the Entomophthoromycotina. Microorganisms 2023; 11:1658. [PMID: 37512833 PMCID: PMC10386553 DOI: 10.3390/microorganisms11071658] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
A meta-analysis based on the published literature was conducted to evaluate the breadth of host ranges of arthropod pathogens in the fungal subphylum Entomophthoromycotina. The majority of pathogens in this subphylum infect insects, although arachnids (especially mites), collembola, and myriapods are also used as hosts. Most species (76%) have specialized host ranges and only infect arthropods in one host family. The breadth of host ranges in the Entomophthoromycotina is generally greater for species in more basal groups (Conidiobolaceae and Neoconidiobolaceae), where most species are soil-borne saprobes and few are pathogens. The Batkoaceae is a transitionary family in which all species are pathogens and both generalists and specialists occur. Among pathogen-infecting insects, Hemiptera and Diptera are the most commonly infected insect orders. Within the Hemiptera, hosts in the suborder Sternorrhycha were infected by more fungal species than the Auchenorrhyncha and Heteroptera.
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Affiliation(s)
- Natalie E Sacco
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Ann E Hajek
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
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8
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Molecular characterization of two novel totiviruses coinfecting the basal fungus Conidiobolus adiaeretus. Arch Virol 2022; 168:7. [PMID: 36542124 DOI: 10.1007/s00705-022-05689-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
A number of viruses have recently been discovered in all major fungal phyla using high-throughput sequencing. However, basal fungi remain among the least-explored organisms with respect to the presence of mycoviruses. In this study, we characterized two mycoviruses coinfecting the basal fungus Conidiobolus adiaeretus, which we have named "Conidiobolus adiaeretus totivirus 1" (CaTV1) and "Conidiobolus adiaeretus totivirus 2" (CaTV2). Due to their similar sizes, the genomic RNAs of these two viruses comigrated as a single band in 1.5% agarose gel electrophoresis but could be distinguished and characterized by next-generation sequencing and RT-PCR. Like those of other totiviruses, the genomes of both CaTV1 and CaTV2 have two discontinuous open reading frames: ORF1 and ORF2, encoding a putative capsid protein and a putative RNA-dependent RNA polymerase (RdRp), respectively. The RdRps of CaTV1 and CaTV2 have 62.73% and 63.76% amino acid sequence identity, respectively, to Wuhan insect virus 26 and have 62.15% amino acid sequence identity to each other. A maximum-likelihood phylogenetic tree based on RdRp amino acid sequences showed that both CaTV1 and CaTV2 clustered in a clade with members of the genus Totivirus. Therefore, we propose that CaTV1 and CaTV2 are two new members of the genus Totivirus in the family Totiviridae.
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The Early Terrestrial Fungal Lineage of Conidiobolus—Transition from Saprotroph to Parasitic Lifestyle. J Fungi (Basel) 2022; 8:jof8080789. [PMID: 36012777 PMCID: PMC9409958 DOI: 10.3390/jof8080789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
Fungi of the Conidiobolus group belong to the family Ancylistaceae (Entomophthorales, Entomophthoromycotina, Zoopagomycota) and include over 70 predominantly saprotrophic species in four similar and closely related genera, that were separated phylogenetically recently. Entomopathogenic fungi of the genus Batkoa are very close morphologically to the Conidiobolus species. Their thalli share similar morphology, and they produce ballistic conidia like closely related entomopathogenic Entomophthoraceae. Ballistic conidia are traditionally considered as an efficient tool in the pathogenic process and an important adaptation to the parasitic lifestyle. Our study aims to reconstruct the phylogeny of this fungal group using molecular and genomic data, ancestral lifestyle and morphological features of the conidiobolus-like group and the direction of their evolution. Based on phylogenetic analysis, some species previously in the family Conidiobolaceae are placed in the new families Capillidiaceae and Neoconidiobolaceae, which each include one genus, and the Conidiobolaceae now includes three genera. Intermediate between the conidiobolus-like groups and Entomophthoraceae, species in the distinct Batkoa clade now belong in the family Batkoaceae. Parasitism evolved several times in the Conidiobolus group and Ancestral State Reconstruction suggests that the evolution of ballistic conidia preceded the evolution of the parasitic lifestyle.
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10
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Zhao H, Nie Y, Zong TK, Wang YJ, Wang M, Dai YC, Liu XY. Species Diversity and Ecological Habitat of Absidia (Cunninghamellaceae, Mucorales) with Emphasis on Five New Species from Forest and Grassland Soil in China. J Fungi (Basel) 2022; 8:jof8050471. [PMID: 35628728 PMCID: PMC9146633 DOI: 10.3390/jof8050471] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 02/05/2023] Open
Abstract
Although species of Absidia are known to be ubiquitous in soil, animal dung, and insect and plant debris, the species diversity of the genus and their ecological habitats have not been sufficiently investigated. In this study, we describe five new species of Absidia from forest and grassland soils in southwestern China, with support provided by phylogenetic, morphological, and physiological evidence. The species diversity and ecological habitat of Absidia are summarized. Currently, 22 species are recorded in China, which mainly occur in soil, especially in tropical and subtropical forests and mountains. An updated key to the species of Absidia in China is also provided herein. This is the first overview of the Absidia ecological habitat.
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Affiliation(s)
- Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China;
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan 243002, China;
| | - Tong-Kai Zong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China;
| | - Yu-Jie Wang
- College of Plant Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; (Y.-J.W.); (M.W.)
| | - Mu Wang
- College of Plant Science, Tibet Agricultural and Animal Husbandry University, Linzhi 860000, China; (Y.-J.W.); (M.W.)
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China;
- Correspondence: (Y.-C.D.); (X.-Y.L.)
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Correspondence: (Y.-C.D.); (X.-Y.L.)
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11
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Nie Y, Zhao H, Wang Z, Zhou Z, Liu X, Huang B. Two new species in Capillidium (Ancylistaceae, Entomophthorales) from China, with a proposal for a new combination. MycoKeys 2022; 89:139-153. [PMID: 36760830 PMCID: PMC9849098 DOI: 10.3897/mycokeys.89.79537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/12/2022] [Indexed: 01/24/2023] Open
Abstract
A taxonomic revision of Conidiobolus s.l. (Ancylistaceae, Entomophthorales) delimited all members that form capilliconidia into the genus Capillidium. In this study, we report two new species of Capillidium that were isolated in China. Capillidiummacrocapilliconidium sp. nov. is characterised by large capilliconidia. Capillidiumjiangsuense sp. nov. is differentiated by large capilliconidia and long, slender secondary conidiophores. Phylogenetic analyses were performed using sequences from the nuclear large subunit of rDNA (nucLSU), the mitochondrial small subunit of rDNA (mtSSU) and elongation-factor-like (EFL). The analyses revealed sister relationships between Ca.macrocapilliconidium sp. nov. and Ca.globuliferus / Ca.pumilum and between Ca.jiangsuense sp. nov. and Ca.denaeosporum. Additionally, a new combination of Ca.rugosum (Drechsler) B. Huang & Y. Nie comb. nov. is proposed herein. An identification key is provided for the ten accepted Capillidium species.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, ChinaAnhui Agricultural UniversityHefeiChina,School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui University of TechnologyMa'anshanChina
| | - Heng Zhao
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaBeijing Forestry UniversityBeijingChina
| | - ZiMin Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui University of TechnologyMa'anshanChina
| | - ZhengYu Zhou
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma,anshan 243002, ChinaAnhui University of TechnologyMa'anshanChina
| | - XiaoYong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, ChinaShandong Normal UniversityJinanChina
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, ChinaAnhui Agricultural UniversityHefeiChina
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12
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Stengel A, Stanke KM, Quattrone AC, Herr JR. Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front Microbiol 2022; 13:847067. [PMID: 35250961 PMCID: PMC8892103 DOI: 10.3389/fmicb.2022.847067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023] Open
Abstract
Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.
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Affiliation(s)
- Ashley Stengel
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kimberly M Stanke
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda C Quattrone
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Joshua R Herr
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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13
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Three New Species of Absidia (Mucoromycota) from China Based on Phylogeny, Morphology and Physiology. DIVERSITY 2022. [DOI: 10.3390/d14020132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Species of Absidia are distributed widely in the environment, while their diversity is insufficiently studied. Three new species, A. frigida, A. gemella and A. longissima, are proposed herein from Xinjiang and Yunnan in China based on phylogenetic, morphological and physiological evidence. According to maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) analyses, the phylogenetical results suggest that A. frigida, A. gemella and A. longissima are closely related to A. psychrophilia, A. turgida and A. zonata and A. koreana, respectively, based on ITS and LSU rDNA sequences. Absidia frigida is characterized by a lower growth temperature, which does not grow above 24 °C. It differs from A. psychrophilia by sporangiophores, sporangia, columellae, collars and projections. Absidia gemella is distinguished from A. turgida by hypha, sporangiospores, sporangia, projections and sporangiophores. Absidia longissima is discriminated from A. zonata and A. koreana by sporangiophores, columellae and collars. The three new species are described and illustrated in this article.
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14
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Möckel L, Meusemann K, Misof B, Schwartze VU, De Fine Licht HH, Voigt K, Stielow B, de Hoog S, Beutel RG, Buellesbach J. Phylogenetic Revision and Patterns of Host Specificity in the Fungal Subphylum Entomophthoromycotina. Microorganisms 2022; 10:microorganisms10020256. [PMID: 35208711 PMCID: PMC8879804 DOI: 10.3390/microorganisms10020256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/04/2023] Open
Abstract
The Entomophthoromycotina, a subphylum close to the root of terrestrial fungi with a bias toward insects as their primary hosts, has been notoriously difficult to categorize taxonomically for decades. Here, we reassess the phylogeny of this group based on conserved genes encoding ribosomal RNA and RNA polymerase II subunits, confirming their general monophyly, but challenging previously assumed taxonomic relationships within and between particular clades. Furthermore, for the prominent, partially human-pathogenic taxon Conidiobolus, a new type species C. coronatus is proposed in order to compensate for the unclear, presumably lost previous type species C. utriculosus Brefeld 1884. We also performed an exhaustive survey of the broad host spectrum of the Entomophthoromycotina, which is not restricted to insects alone, and investigated potential patterns of co-evolution across their megadiverse host range. Our results suggest multiple independent origins of parasitism within this subphylum and no apparent co-evolutionary events with any particular host lineage. However, Pterygota (i.e., winged insects) clearly constitute the most dominantly parasitized superordinate host group. This appears to be in accordance with an increased dispersal capacity mediated by the radiation of the Pterygota during insect evolution, which has likely greatly facilitated the spread, infection opportunities, and evolutionary divergence of the Entomophthoromycotina as well.
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Affiliation(s)
- Lars Möckel
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany; (L.M.); (V.U.S.); (K.V.)
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Karen Meusemann
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, 53113 Bonn, Germany; (K.M.); (B.M.)
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, 53113 Bonn, Germany; (K.M.); (B.M.)
| | - Volker U. Schwartze
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany; (L.M.); (V.U.S.); (K.V.)
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Henrik H. De Fine Licht
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark;
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany; (L.M.); (V.U.S.); (K.V.)
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Benjamin Stielow
- Center of Expertise in Mycology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (B.S.); (S.d.H.)
- Westerdijk Fungal Biodiversity Institute—KNAW, 3584 CT Utrecht, The Netherlands
| | - Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (B.S.); (S.d.H.)
- Westerdijk Fungal Biodiversity Institute—KNAW, 3584 CT Utrecht, The Netherlands
| | - Rolf G. Beutel
- Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Jan Buellesbach
- Institute for Evolution & Biodiversity, University of Münster, 48149 Münster, Germany
- Correspondence: ; Tel.: +49-(0)-251-83-21637
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15
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Cai Y, Nie Y, Zhao H, Wang Z, Zhou Z, Liu X, Huang B. Azygosporus gen. nov., a synapmorphic clade in the family Ancylistaceae. MycoKeys 2021; 85:161-172. [PMID: 35068985 PMCID: PMC8741705 DOI: 10.3897/mycokeys.85.73405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/30/2021] [Indexed: 11/15/2022] Open
Abstract
The fungal genus Conidiobolus sensu lato was delimited into four genera based on morphology and phylogeny. However, the taxonomic placement of C.parvus has not been determined until now. Here, we show that C.parvus belongs to a distinct lineage based on mitochondrial (mtSSU) and nuclear (TEF1 and nrLSU) phylogenetic analyses. Phylogenetic analyses further revealed a new species as sister to C.parvus. We identified a synapomorphy uniting these lineages (azygospore production) that was not observed in other allied genera of the family Ancylistaceae, and erected a new genus Azygosporusgen. nov. for this monophyletic group, with a new combination, A.parvuscomb. nov. as the type species. Within Azygosporus, the novel species A.macropapillatussp. nov. was introduced from China based on morphological characteristics and molecular evidence, which is characterized by its prominent basal papilla, in comparison to other closely related species, measuring 7.5–10.0×5.0–10.0 µm. Our study resolved the phylogenetic placement of C.parvus and improved the taxonomic system of the Ancylistaceae family.
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16
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Souza DA, Oliveira CMD, Tamai MA, Faria M, Lopes RB. First report on the natural occurrence of entomopathogenic fungi in populations of the leafhopper Dalbulus maidis (Hemiptera: Cicadellidae): Pathogen identifications and their incidence in maize crops. Fungal Biol 2021; 125:980-988. [PMID: 34776235 DOI: 10.1016/j.funbio.2021.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
The corn leafhopper Dalbulus maidis is one of the most important pests of maize in Latin America. Here we report, for the first time, the natural occurrence of two fungal species infecting the adult stage of this pest. In 2020, insects killed by a pale bluish green fungus in irrigated maize fields located in Northeast Brazil were found attached to the abaxial surface of leaves. Using morphological characters and multigenic phylogeny, it was identified as Metarhizium brasiliense. In the beginning of 2021, the same pathogen was seen on adults in a maize field in the Central-Western region, alongside an entomophthoralean fungus during an epizootic. The latter pathogen was molecularly identified as a species in the genus Batkoa. The number of Batkoa-infected leafhoppers, displaying the typical swollen abdomen and extended wings, reached an average of 1.88 per maize leaf (86.42% of the sampled adults). The incidence of M. brasiliense was higher in plots in the Northeastern region (0.22 and 0.53 adult per leaf) when compared to the Central-Western region (0.04 adult per leaf). The report of D. maidis adults infected by M. brasiliense in agricultural settings located in different geographic regions and over 550 km apart indicates probable widespread occurrence of this pathogen in Brazil. Moreover, this opens the possibility of more applied biological control studies and, perhaps, the development of new tools to manage D. maidis populations.
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Affiliation(s)
- Daniela Aguiar Souza
- Embrapa Genetic Resources and Biotechnology, PqEB W5 North Avenue, Brasília Federal District, 70770-917, Brazil
| | | | - Marco Antonio Tamai
- Bahia State University, UNEB, BR 242 Road km 4, Barreiras, Bahia, 47800-000, Brazil
| | - Marcos Faria
- Embrapa Genetic Resources and Biotechnology, PqEB W5 North Avenue, Brasília Federal District, 70770-917, Brazil
| | - Rogerio Biaggioni Lopes
- Embrapa Genetic Resources and Biotechnology, PqEB W5 North Avenue, Brasília Federal District, 70770-917, Brazil.
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17
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Nie Y, Zhao H, Wang Z, Zhou Z, Liu X, Huang B. The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus. Front Microbiol 2021; 12:765733. [PMID: 34858376 PMCID: PMC8632527 DOI: 10.3389/fmicb.2021.765733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022] Open
Abstract
The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zimin Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Zhengyu Zhou
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Xiaoyong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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18
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Nie Y, Wang ZM, Liu XY, Huang B. A morphological and molecular survey of Neoconidiobolus reveals a new species and two new combinations. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Nie Y, Wang ZM, Zhao H, Liu XY, Huang B. Complete mitochondrial genome of Neoconidiobolus thromboides ( Entomophthorales: Ancylistaceae). Mitochondrial DNA B Resour 2021; 6:1840-1841. [PMID: 34124362 PMCID: PMC8183557 DOI: 10.1080/23802359.2021.1934167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/14/2021] [Indexed: 10/27/2022] Open
Abstract
Neoconidiobolus thromboides is a pandemic species in the genus Neoconidiobolus. In this article, we report the first complete sequence of mitochondrial genome from a common entomophthoroid fungus Neoconidiobolus thromboides under Illumina next-generation sequencing system. The total length of the mitogenome is 34,984 bp with a GC content of 26.99%. The gene annotation revealed 56 genes, including 30 protein-coding genes (PCGs), two ribosomal RNA genes (rDNAs), 24 transfer RNA (tRNA) genes. Phylogenetic analyses of 14 concatenated conserved PCGs indicated that N. thromboides was grouped with Capillidium heterosporum and Conidiobolus sp.
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Affiliation(s)
- Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan, China
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Zi-Min Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan, China
| | - Heng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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20
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Cai Y, Nie Y, Wang ZM, Huang B. The complete mitochondrial genome of Microconidiobolus nodosus ( Entomophthorales: Ancylistaceae). Mitochondrial DNA B Resour 2021; 6:1743-1744. [PMID: 34104757 PMCID: PMC8158263 DOI: 10.1080/23802359.2021.1930219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, the complete mitochondrial genome of Microconidiobolus nodosus was sequenced which is the first mitochondrial genome of the genus. The mitochondrial genome is 31,638 bp long and 27.18% in GC ratio, and it contains 14 conserved protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis showed that M. nodosus was closely related to Conodiobolus sp. This study reported the whole mitochondrial genome and character of a basal fungus M .nodosus and provided a better understanding of the phylogeny of basal fungi.
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Affiliation(s)
- Yue Cai
- College of Biology, Food and Environment, Hefei University, Hefei, China
| | - Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
- School of Civil Engineering and Architecture, Anhui University of Technology, China
| | - Zi-Min Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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21
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Molecular characterization of a novel totivirus infecting the basal fungus Conidiobolus heterosporus. Arch Virol 2021; 166:1801-1804. [PMID: 33866414 DOI: 10.1007/s00705-021-05054-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/09/2021] [Indexed: 10/21/2022]
Abstract
Mycoviruses are widely distributed in fungi, but only a few mycoviruses have been reported in basal fungi to date. Here, we characterized a novel totivirus isolated from the basal fungus Conidiobolus heterosporus, and we designated this virus as "Conidiobolus heterosporus totivirus 1" (ChTV1). The complete genome of ChTV1 contains two discontinuous open reading frames (ORFs), ORF1 and ORF2, encoding a putative coat protein (CP) and a putative RNA-dependent RNA polymerase (RdRP), respectively. Phylogenetic analysis based on RdRP sequences showed that ChTV1 clustered with members of the genus Totivirus. The RdRP of ChTV1 has 51% sequence identity to that of Trichoderma koningiopsis totivirus 1 (TkTV1), which is the highest among mycoviruses. However, TkTV1 formed a distinct cluster with Wuhan insect virus 27, with 63% RdRP sequence identity, although Wuhan insect virus 27 has not been described, and its host represents a different kingdom. Therefore, we propose that ChTV1 is a new member of the genus Totivirus, family Totiviridae.
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22
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Zhao H, Zhu J, Zong TK, Liu XL, Ren LY, Lin Q, Qiao M, Nie Y, Zhang ZD, Liu XY. Two New Species in the Family Cunninghamellaceae from China. MYCOBIOLOGY 2021; 49:142-150. [PMID: 37970189 PMCID: PMC10635138 DOI: 10.1080/12298093.2021.1904555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/19/2021] [Accepted: 03/14/2021] [Indexed: 11/17/2023]
Abstract
The species within the family Cunninghamellaceae are widely distributed and produce important metabolites. Morphological studies along with a molecular phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) of ribosomal DNA revealed two new species in this family from soils in China, that is, Absidia ovalispora sp. nov. and Cunninghamella globospora sp. nov. The former is phylogenetically closely related to Absidia koreana, but morphologically differs in sporangiospores, sporangia, sporangiophores, columellae, collars, and rhizoids. The latter is phylogenetically closely related to Cunninghamella intermedia, but morphologically differs in sporangiola and colonies. They were described and illustrated.
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Affiliation(s)
- Heng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhu
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Tong-Kai Zong
- College of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Xiao-Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Ying Ren
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Qing Lin
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Min Qiao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Zhi-Dong Zhang
- Xinjiang Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiao-Yong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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23
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Claussen M, Schmidt S. Differentiation of Basidiobolus spp. Isolates: RFLP of a Diagnostic PCR Amplicon Matches Sequence-Based Classification and Growth Temperature Preferences. J Fungi (Basel) 2021; 7:110. [PMID: 33546095 PMCID: PMC7913143 DOI: 10.3390/jof7020110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/01/2021] [Accepted: 01/07/2021] [Indexed: 11/20/2022] Open
Abstract
The genus Basidiobolus, known since 1886, is primarily associated with reptiles and amphibians. Although globally distributed, rare infections caused by members of this genus mainly occur in tropical and subtropical regions. Morphological and physiological characteristics were used in the past for the description of species. However, some of these characteristics vary depending on culture conditions. Therefore, most species names are regarded as synonyms of B. ranarum as the only pathogenic species. Yet, not all environmental isolates are necessarily pathogenic. This study aimed to analyze if environmental Basidiobolus isolates can be distinguished reliably based on morpho-physiological and molecular characteristics. Eleven isolates originally obtained from feces of south African reptiles and one type strain, Basidiobolus microsporus DSM 3120, were examined morpho-physiologically. Sequence analysis of the 18S and partial 28S rRNA gene and restriction analysis of a diagnostic amplicon (restriction fragment length polymorphism, RFLP) were performed for all 12 strains. Based on the results obtained, morphological features and the 18S rRNA sequence proved insufficient for the reliable differentiation of isolates. However, isolates were distinguishable by growth temperature profiles, which matched isolate clusters established by partial 28S rRNA gene sequence and restriction analysis of a Basidiobolus specific diagnostic PCR amplicon. Our results indicate that RFLP analysis can be used as a fast screening method to identify Basidiobolus isolates with similar physiological characteristics.
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Affiliation(s)
- Maike Claussen
- School of Life Sciences, Discipline of Microbiology, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa;
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24
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Goffre D, Jensen AB, Lopez Lastra CC, Humber RA, Folgarait PJ. Conidiobolus lunulus, a new entomophthoralean species isolated from leafcutter ants. Mycologia 2020; 113:56-64. [PMID: 33151805 DOI: 10.1080/00275514.2020.1816387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Entomophthoralean fungi with pathogenic abilities to infect social insects are rare. Here, we describe a fungus isolated from leafcutter ants. Morphologically, the fungus has spherical primary conidia and two types of microconidia: one with the same shape as the primary conidia and another with an elliptical to half-moon shape. The fungus also produces villose conidia known previously only from Conidiobolus coronatus. A multilocus phylogenetic analysis was performed with nuc rDNA sequences from three regions (28S, 18S, and internal transcribed spacer [ITS]). Our isolates are distinguished as a new species, described here as Conidiobolus lunulus, and is more closely related to C. brefeldianus than to C. coronatus, despite the greater morphological resemblance to the latter. Morphological differences, unique phylogenetic placement, and isolation from an altogether new host support this finding. This is the first record of an entomophthoralean species isolated from leafcutter ants.
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Affiliation(s)
- D Goffre
- Ants Laboratory, Department of Science and Technology, Quilmes National University , CONICET, Roque Saenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - A B Jensen
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg Campus , Copenhagen, Denmark
| | - C C Lopez Lastra
- Centro de Estudios Parasitológicos y de Vectores, CONICET-Universidad Nacional de La Plata , La Plata, Argentina
| | - R A Humber
- Emerging Pests and Pathogens Research, Robert W. Holley Center for Agriculture and Health , Ithaca, New York 14853
| | - P J Folgarait
- Ants Laboratory, Department of Science and Technology, Quilmes National University , CONICET, Roque Saenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
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25
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Nie Y, Cai Y, Gao Y, Yu DS, Wang ZM, Liu XY, Huang B. Three new species of Conidiobolus sensu stricto from plant debris in eastern China. MycoKeys 2020; 73:133-149. [PMID: 33117082 PMCID: PMC7561611 DOI: 10.3897/mycokeys.73.56905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 11/12/2022] Open
Abstract
The genus Conidiobolus Bref. is widely distributed and the Conidiobolus sensu lato contained three other genera, Capillidium, Microconidiobolus and Neoconidiobolus. A molecular phylogeny based on the nuclear large subunit of rDNA (nucLSU), the mitochondrial small subunit of rDNA (mtSSU) and the translation elongation factor 1-alpha gene (TEF1) revealed three novel species within the clade of Conidiobolus s.s., i.e. C. bifurcatus sp. nov., C. taihushanensis sp. nov. and C. variabilis sp. nov. These three species were isolated from plant debris in eastern China. Morphologically, C. bifurcatus sp. nov. is characterised by its secondary conidiophores often branched at the tip to form two short stipes each bearing a secondary conidium. C. taihushanensis sp. nov. is different from the others in its straight apical mycelia and the production of 2-5 conidia. C. variabilis sp. nov. is distinctive because of its various shapes of primary conidia. All these three new taxa are illustrated herein with an update key to the species of the genus Conidiobolus s.s.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China.,School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan 243002, China
| | - Yue Cai
- Department of Biological and Environmental Engineering, Hefei University, Hefei 230601, China
| | - Yang Gao
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, Nanchang, 330045, China
| | - De-Shui Yu
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
| | - Zi-Min Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan 243002, China
| | - Xiao-Yong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei 230036, China
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26
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Wang Y, Nie Y, Yu D, Xie X, Qin L, Yang Y, Huang B. Genome-wide study of saprotrophy-related genes in the basal fungus Conidiobolus heterosporus. Appl Microbiol Biotechnol 2020; 104:6261-6272. [PMID: 32445001 DOI: 10.1007/s00253-020-10698-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/03/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
Conidiobolus spp. are important saprophytic basal fungi. However, to date, no genomic-level data for decaying plant materials in the genus Conidiobolus has been reported. Here, we report that the 33.4-Mb genome of Conidiobolus heterosporus encodes 10,857 predicted genes. Conidiobolus heterosporus harbors 394 CAZyme-encoding genes belonging to 4 major modules but does not encode a polysaccharide lyase (PL). Many carbohydrate esterases (CEs) belonging to the family CE12 play crucial roles as pectin acetylesterases, and 14 genes were upregulated in the IM (fungus grown on inducing medium) among 17 expressed CE12 family genes. In addition, most of the genes in the GH132 CAZyme family showed a greater than 5-fold increase in expression in the IM compared with that in the wild type. Furthermore, 122 P450-encoding genes grouped into 11 families were detected in the fungal genome, most of which belonged to the CYP547 family (36 genes) followed by CYP548 (27 genes) and CYP5856 (25 genes). Interestingly, members of the families CYP5014 and CYP5136 were identified, the first time such enzymes have been described in a fungus. Our findings provide new insights into the genomics and genomic features of the saprophytic basal fungus C. heterosporus.Key Points• Genome of the saprobiotic basal fungus C. heterosporus was sequenced and analyzed.• 394 CAZymes but no PL family genes were found and expression levels were determined.• CE12 and GH132 proteins may play roles in the pectin and plant material degradation.• A large number of P450s but few P450 families existed in the fungus.
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Affiliation(s)
- Yulong Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China
| | - Yong Nie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China.,School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan, 243002, China
| | - Deshui Yu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China
| | - Xiangyun Xie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China
| | - Li Qin
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China
| | - Yang Yang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China. .,Engineering Research Center of Fungal Biotechnology, Ministry of Education, Anhui Agricultural University, Hefei, 230036, China.
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