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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 PMCID: PMC11298794 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 Research Campus Drive, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R. Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R. Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J. Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V. Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A. B. Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža Čadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H. DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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Liu T, Pyle AM. Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi. J Mol Biol 2024; 436:168513. [PMID: 38447889 DOI: 10.1016/j.jmb.2024.168513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Systemic fungal infections are a growing public health threat, and yet viable antifungal drug targets are limited as fungi share a similar proteome with humans. However, features of RNA metabolism and the noncoding transcriptomes in fungi are distinctive. For example, fungi harbor highly structured RNA elements that humans lack, such as self-splicing introns within key housekeeping genes in the mitochondria. However, the location and function of these mitochondrial riboregulatory elements has largely eluded characterization. Here we used an RNA-structure-based bioinformatics pipeline to identify the group I introns interrupting key mitochondrial genes in medically relevant fungi, revealing their fixation within a handful of genetic hotspots and their ubiquitous presence across divergent phylogenies of fungi, including all highest priority pathogens such as Candida albicans, Candida auris, Aspergillus fumigatus and Cryptococcus neoformans. We then biochemically characterized two representative introns from C. albicans and C. auris, demonstrating their exceptionally efficient splicing catalysis relative to previously-characterized group I introns. Indeed, the C. albicans mitochondrial intron displays extremely rapid catalytic turnover, even at ambient temperatures and physiological magnesium ion concentrations. Our results unmask a significant new set of players in the RNA metabolism of pathogenic fungi, suggesting a promising new type of antifungal drug target.
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Affiliation(s)
- Tianshuo Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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Shin TY, Kim S, Heo I, Woo SD, Kim WJ. The complete mitogenome of the entomopathogenic fungus Metarhizium pinghaense 15R. Mitochondrial DNA B Resour 2023; 8:1411-1415. [PMID: 38515796 PMCID: PMC10956925 DOI: 10.1080/23802359.2023.2292145] [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: 02/27/2023] [Accepted: 12/03/2023] [Indexed: 03/23/2024] Open
Abstract
In this study, the complete mitogenome of the entomopathogenic fungus Metarhizium pinghaense 15 R, which is highly virulent to aphids and was isolated from Korean soil, was assembled and annotated for three ATP synthase subunits (atp6, atp8, and atp9), three cytochrome oxidase subunits (cox1, cox2, and cox3), apocytochrome b (cob), seven subunits of NADH dehydrogenase (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), two ribosomal RNAs (rnl and rns), and 19 tRNA genes. Five genes were carrying a total of eight introns, and they may encode ribosomal protein S3, LAGLIDADG and GIY-YIG endonucleases. Phylogenetic analysis based on the mitochondrial nucleotide sequence confirmed that the M. pinghaense 15 R is a member of the Clavicipitaceae, and is closely related to the species M. anisopliae, M. robertsii, and M. brunneum. The mtDNA base sequence of the M. pinghaense 15 R strain reported in this study is thought to be useful for biological resource genetic data.
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Affiliation(s)
- Tae Young Shin
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, Korea
| | - Seulki Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, Korea
| | - InJi Heo
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, Korea
| | - Soo Dong Woo
- Department of Agricultural Biology, College of Agriculture, Life & Environment Science, Chungbuk National University, Cheongju, Korea
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Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [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: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
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Ye L, He X, Su C, Feng H, Meng G, Chen B, Wu X. The Effect of Mitochondria on Ganoderma lucidum Growth and Bioactive Components Based on Transcriptomics. J Fungi (Basel) 2022; 8:1182. [PMID: 36354949 PMCID: PMC9692720 DOI: 10.3390/jof8111182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 01/06/2024] Open
Abstract
Mitochondria are the power source of living cells and implicated in the oxidative metabolism. However, the effect of mitochondria on breeding is usually ignored in conventional research. In this study, the effect of mitochondria on Ganoderma lucidum morphology, yield, and main primary bioactive components was analyzed via structuring and comparing isonuclear alloplasmic strains. The crucial biological pathways were then explored based on the transcriptome. The results showed that isonuclear alloplasmic exhibited difference in mycelial growth rate in potato dextrose agar medium (PDA), basidiospore yield, and polysaccharide and triterpenoid content. Otherwise, mitochondria did not change colony and fruit body morphology, mushroom yield, or mycelial growth rate in solid-state fermentation cultivation material. The transcriptome data of two significant isonuclear alloplasmic strains S1 and S5 revealed that the involvement of differentially expressed genes (DEGs) was mainly in pentose and glucuronate interconversions, starch and sucrose metabolism, and steroid biosynthesis. The result was further confirmed by the other isonuclear alloplasmic strains. The above results further proved that mitochondria could affect the active components of G. lucidum. Our results provide information which will contribute to understanding of mitochondria and will be helpful for breeding improved varieties.
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Affiliation(s)
- Liyun Ye
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofang He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Congbao Su
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haiying Feng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoliang Meng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bingzhi Chen
- College of Food Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Subtropical Characteristic Fruits, Vegetables and Edible Fungi Processing (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Fuzhou 350002, China
| | - Xiaoping Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Li Q, Zhang T, Li L, Bao Z, Tu W, Xiang P, Wu Q, Li P, Cao M, Huang W. Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus Ganoderma. J Fungi (Basel) 2022; 8:jof8080781. [PMID: 35893149 PMCID: PMC9394262 DOI: 10.3390/jof8080781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
- Correspondence: (M.C.); (W.H.); Tel.: +86-028-84592187 (W.H.)
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
- Correspondence: (M.C.); (W.H.); Tel.: +86-028-84592187 (W.H.)
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Degradi L, Tava V, Prigitano A, Esposto MC, Tortorano AM, Saracchi M, Kunova A, Cortesi P, Pasquali M. Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients. Microorganisms 2022; 10:microorganisms10061115. [PMID: 35744633 PMCID: PMC9227538 DOI: 10.3390/microorganisms10061115] [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: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium musae has recently been described as a cross-kingdom pathogen causing post-harvest disease in bananas and systemic and superficial infection in humans. The taxonomic identity of fungal cross-kingdom pathogens is essential for confirming the identification of the species on distant infected hosts. Understanding the level of variability within the species is essential to decipher the population homogeneity infecting human and plant hosts. In order to verify that F. musae strains isolated from fruits and patients are part of a common population and to estimate their overall diversity, we assembled, annotated and explored the diversity of the mitogenomes of 18 F. musae strains obtained from banana fruits and human patients. The mitogenomes showed a high level of similarity among strains with different hosts’ origins, with sizes ranging from 56,493 to 59,256 bp. All contained 27 tRNA genes and 14 protein-coding genes, rps3 protein, and small and large ribosomal subunits (rns and rnl). Variations in the number of endonucleases were detected. A comparison of mitochondrial endonucleases distribution with a diverse set of Fusarium mitogenomes allowed us to specifically discriminate F. musae from its sister species F. verticillioides and the other Fusarium species. Despite the diversity in F. musae mitochondria, strains from bananas and strains from human patients group together, indirectly confirming F. musae as a cross-kingdom pathogen.
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Affiliation(s)
- Luca Degradi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Valeria Tava
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Maria Carmela Esposto
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Anna Maria Tortorano
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy; (A.P.); (M.C.E.); (A.M.T.)
| | - Marco Saracchi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Andrea Kunova
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Paolo Cortesi
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy; (L.D.); (V.T.); (M.S.); (A.K.); (P.C.)
- Correspondence:
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Zhong C, Jin J, Zhou R, Liu H, Xie J, Wan D, Xiao S, Zhang S. Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi. Ecol Evol 2022; 12:e8818. [PMID: 35494498 PMCID: PMC9036042 DOI: 10.1002/ece3.8818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/23/2022] Open
Abstract
Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of Ophiocordyceps xuefengensis, in addition to comparing it against other three complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the Ophiocordyceps sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis. Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.
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Affiliation(s)
- Can Zhong
- Horticulture and Landscape College Hunan Agricultural University Changsha China.,Institute of Chinese Materia Medica Hunan Academy of Chinese Medicine Changsha China
| | - Jian Jin
- Institute of Chinese Materia Medica Hunan Academy of Chinese Medicine Changsha China
| | - Rongrong Zhou
- Changchun University of Chinese Medicine Changchun China
| | - Hao Liu
- Institute of Chinese Materia Medica Hunan Academy of Chinese Medicine Changsha China
| | - Jing Xie
- Institute of Chinese Materia Medica Hunan Academy of Chinese Medicine Changsha China
| | - Dan Wan
- Institute of Chinese Materia Medica Hunan Academy of Chinese Medicine Changsha China
| | - Shengen Xiao
- Horticulture and Landscape College Hunan Agricultural University Changsha China
| | - Shuihan Zhang
- Horticulture and Landscape College Hunan Agricultural University Changsha China.,Institute of Chinese Materia Medica Hunan Academy of Chinese Medicine Changsha China
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9
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Buslyk TV, Rosalovsky VP, Salyha YT. PCR-Based Detection and Quantification of Mycotoxin-Producing Fungi. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Fonseca PLC, De-Paula RB, Araújo DS, Tomé LMR, Mendes-Pereira T, Rodrigues WFC, Del-Bem LE, Aguiar ERGR, Góes-Neto A. Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements. Front Microbiol 2021; 12:787283. [PMID: 34925295 PMCID: PMC8672057 DOI: 10.3389/fmicb.2021.787283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023] Open
Abstract
Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0–39) introns, 8.0 (0–100) HEGs, and 8.2 (0–102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.
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Affiliation(s)
- Paula L C Fonseca
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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11
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Wyrębek J, Molcan T, Myszczyński K, van Diepeningen AD, Stakheev AA, Żelechowski M, Bilska K, Kulik T. Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto. Front Microbiol 2021; 12:714651. [PMID: 34531839 PMCID: PMC8439580 DOI: 10.3389/fmicb.2021.714651] [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: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.
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Affiliation(s)
- Joanna Wyrębek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Alexander A Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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12
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Salgado-Salazar C, Skaltsas DN, Phipps T, Castlebury LA. Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. G3-GENES GENOMES GENETICS 2021; 11:6163289. [PMID: 33693679 DOI: 10.1093/g3journal/jkab071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/25/2021] [Indexed: 11/14/2022]
Abstract
Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.
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Affiliation(s)
- Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
| | - Demetra N Skaltsas
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37831, USA
| | - Tunesha Phipps
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
| | - Lisa A Castlebury
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
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13
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de Almeida JR, Riaño Pachón DM, Franceschini LM, dos Santos IB, Ferrarezi JA, de Andrade PAM, Monteiro-Vitorello CB, Labate CA, Quecine MC. Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes. PLoS One 2021; 16:e0248054. [PMID: 33705433 PMCID: PMC7951889 DOI: 10.1371/journal.pone.0248054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.
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Affiliation(s)
- Jaqueline Raquel de Almeida
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Livia Maria Franceschini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Isaneli Batista dos Santos
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jessica Aparecida Ferrarezi
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Pedro Avelino Maia de Andrade
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Carlos Alberto Labate
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
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14
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Araújo DS, De-Paula RB, Tomé LMR, Quintanilha-Peixoto G, Salvador-Montoya CA, Del-Bem LE, Badotti F, Azevedo VAC, Brenig B, Aguiar ERGR, Drechsler-Santos ER, Fonseca PLC, Góes-Neto A. Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames. Mitochondrion 2021; 58:1-13. [PMID: 33582235 DOI: 10.1016/j.mito.2021.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.
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Affiliation(s)
- Daniel S Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luiz M R Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R G R Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Paula L C Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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15
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Kortsinoglou AM, Saud Z, Eastwood DC, Butt TM, Kouvelis VN. The mitochondrial genome contribution to the phylogeny and identification of Metarhizium species and strains. Fungal Biol 2020; 124:845-853. [PMID: 32948272 DOI: 10.1016/j.funbio.2020.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/24/2020] [Indexed: 12/31/2022]
Abstract
The genus Metarhizium is composed of entomopathogenic fungal biological control agents (BCAs) used for invertebrate pest control. The phylogenetic relationships of species within this genus are still under scrutiny as several cryptic species can be found. In this work, the mitochondrial (mt) genome of Metarhizium brunneum ARSEF 4556 was fully sequenced and a comparative genome analysis was conducted with 7 other available mt genomes, belonging to 5 Metarhizium species: M. anisopliae, M. brunneum, M. robertsii, M. guizhouense and M. majus. Results showed that Metarhizium demonstrates greater conserved stability than other fungal mt genomes. Furthermore, this analysis located 7 diverse regions in both intergenic domains and gene fragments which were ideal for species/strain discrimination. The sequencing of these regions revealed several SNPs among 38 strains tested, 11 of which were uncharacterized. Single gene phylogenies presented variable results which may be used further for intra-species discrimination. Phylogenetic trees based on the concatenation of mt domains and the nuclear ITS1-5.8S-ITS2 region showed discrimination of the species studied and allowed the identification of uncharacterized strains. These were mostly placed within species M. anisopliae and M. brunneum. Five strains clustered together in a clade related to M. brunneum, suggesting that they comprise a cryptic species.
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Affiliation(s)
- Alexandra M Kortsinoglou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
| | - Zack Saud
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, United Kingdom.
| | - Dan C Eastwood
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, United Kingdom.
| | - Tariq M Butt
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, SA2 8PP, Wales, United Kingdom.
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
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16
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Brankovics B, van Diepeningen AD, de Hoog GS, van der Lee TAJ, Waalwijk C. Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics. Front Microbiol 2020; 11:1092. [PMID: 32582074 PMCID: PMC7285627 DOI: 10.3389/fmicb.2020.01092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/30/2020] [Indexed: 11/18/2022] Open
Abstract
The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob, which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators to detect interspecies gene flow.
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Affiliation(s)
- Balázs Brankovics
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Anne D van Diepeningen
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - G Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, KNAW, Utrecht, Netherlands.,Center of Expertise in Mycology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Theo A J van der Lee
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Cees Waalwijk
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
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17
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Kulik T, Brankovics B, van Diepeningen AD, Bilska K, Żelechowski M, Myszczyński K, Molcan T, Stakheev A, Stenglein S, Beyer M, Pasquali M, Sawicki J, Wyrȩbek J, Baturo-Cieśniewska A. Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes. Front Microbiol 2020; 11:1002. [PMID: 32528440 PMCID: PMC7263005 DOI: 10.3389/fmicb.2020.01002] [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: 02/19/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Balazs Brankovics
- Biointeractions & Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina.,Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
| | - Marco Beyer
- Department of Environmental Research and Innovation, Agro-Environmental Systems, Luxembourg Institute of Science and Technology, Belval, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Joanna Wyrȩbek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Baturo-Cieśniewska
- Laboratory of Phytopathology and Molecular Mycology, Department of Biology and Plant Protection, UTP University of Science and Technology, Bydgoszcz, Poland
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18
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Ponts N, Gautier C, Gouzy J, Pinson-Gadais L, Foulongne-Oriol M, Ducos C, Richard-Forget F, Savoie JM, Zhao C, Barroso G. Evolution of Fusarium tricinctum and Fusarium avenaceum mitochondrial genomes is driven by mobility of introns and of a new type of palindromic microsatellite repeats. BMC Genomics 2020; 21:358. [PMID: 32397981 PMCID: PMC7218506 DOI: 10.1186/s12864-020-6770-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
Background Increased contamination of European and Asian wheat and barley crops with “emerging” mycotoxins such as enniatins or beauvericin, produced by Fusarium avenaceum and Fusarium tricinctum, suggest that these phylogenetically close species could be involved in future food-safety crises. Results The mitochondrial genomes of F. tricinctum strain INRA104 and F. avenaceum strain FaLH27 have been annotated. A comparative analysis was carried out then extended to a set of 25 wild strains. Results show that they constitute two distinct species, easily distinguished by their mitochondrial sequences. The mitochondrial genetic variability is mainly located within the intergenic regions. Marks of variations show they have evolved (i) by Single Nucleotide Polymorphisms (SNPs), (ii) by length variations mediated by insertion/deletion sequences (Indels), and (iii) by length mutations generated by DNA sliding events occurring in mononucleotide (A)n or (T)n microsatellite type sequences arranged in a peculiar palindromic organization. The optionality of these palindromes between both species argues for their mobility. The presence of Indels and SNPs in palindrome neighbouring regions suggests their involvement in these observed variations. Moreover, the intraspecific and interspecific variations in the presence/absence of group I introns suggest a high mobility, resulting from several events of gain and loss during short evolution periods. Phylogenetic analyses of intron orthologous sequences suggest that most introns could have originated from lateral transfers from phylogenetically close or distant species belonging to various Ascomycota genera and even to the Basidiomycota fungal division. Conclusions Mitochondrial genome evolution between F. tricinctum and F. avenaceum is mostly driven by two types of mobile genetic elements, implicated in genome polymorphism. The first one is represented by group I introns. Indeed, both genomes harbour optional (inter- or intra-specifically) group I introns, all carrying putatively functional hegs, arguing for a high mobility of these introns during short evolution periods. The gain events were shown to involve, for most of them, lateral transfers between phylogenetically distant species. This study has also revealed a new type of mobile genetic element constituted by a palindromic arrangement of (A) n and (T) n microsatellite sequences whose presence was related to occurrence of SNPs and Indels in the neighbouring regions.
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Affiliation(s)
- Nadia Ponts
- INRAE, MycSA, F-33882, Villenave d'Ornon, France
| | | | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | | | | | | | - Chen Zhao
- Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Gérard Barroso
- INRAE, MycSA, F-33882, Villenave d'Ornon, France. .,University of Bordeaux, INRAE, MycSA, F-33882, Villenave d'Ornon, France.
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19
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Yang M, Zhang H, van der Lee TAJ, Waalwijk C, van Diepeningen AD, Feng J, Brankovics B, Chen W. Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum. Front Microbiol 2020; 11:839. [PMID: 32431686 PMCID: PMC7214670 DOI: 10.3389/fmicb.2020.00839] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/07/2020] [Indexed: 11/26/2022] Open
Abstract
Fusarium asiaticum is one of the pivotal members of the Fusarium graminearum species complex (FGSC) causing Fusarium head blight (FHB) on wheat, barley and rice in large parts of Asia. Besides resulting in yield losses, FHB also causes the accumulation of mycotoxins such as nivalenol (NIV) and deoxynivalenol (DON). The aim of this study was to conduct population studies on F. asiaticum from Southern China through mitochondrial genome analyses. All strains were isolated from wheat or rice from several geographic areas in seven provinces in Southern China. Based on geographic location and host, 210 isolates were selected for next generation sequencing, and their mitogenomes were assembled by GRAbB and annotated to explore the mitochondrial genome variability of F. asiaticum. The F. asiaticum mitogenome proves extremely conserved and variation is mainly caused by absence/presence of introns harboring homing endonuclease genes. These variations could be utilized to develop molecular markers for track and trace of migrations within and between populations. This study illustrates how mitochondrial introns can be used as markers for population genetic analysis. SNP analysis demonstrate the occurrence of mitochondrial recombination in F. asiaticum as was previously found for F. oxysporum and implied for F. graminearum. Furthermore, varying degrees of genetic diversity and recombination showed a high association with different geographic regions as well as with cropping systems. The mitogenome of F. graminearum showed a much higher SNP diversity while the interspecies intron variation showed no evidence of gene flow between the two closely related and sexual compatible species.
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Affiliation(s)
- Meixin Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China.,Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Balázs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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20
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Fonseca PLC, Badotti F, De-Paula RB, Araújo DS, Bortolini DE, Del-Bem LE, Azevedo VA, Brenig B, Aguiar ERGR, Góes-Neto A. Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes. Front Microbiol 2020; 11:765. [PMID: 32411111 PMCID: PMC7202290 DOI: 10.3389/fmicb.2020.00765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/30/2020] [Indexed: 12/24/2022] Open
Abstract
The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.
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Affiliation(s)
- Paula L. C. Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B. De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Daniel S. Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Dener E. Bortolini
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A. Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R. G. R. Aguiar
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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21
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Shen T, Wang Q, Li C, Zhou B, Li Y, Liu Y. Transcriptome sequencing analysis reveals silver nanoparticles antifungal molecular mechanism of the soil fungi Fusarium solani species complex. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:122063. [PMID: 31972432 DOI: 10.1016/j.jhazmat.2020.122063] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/08/2020] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Silver nanoparticles (AgNPs) have been widely used in various fields due to their antimicrobial activities. However, the antimicrobial mechanisms of AgNPs against fungi, especially on transcriptional level, are still unclear. In this study, the inhibitory property of AgNPs against Fusarium solani species complex was investigated. Transmission electron microscopes were used to observe the alterations in morphology and cellular structure of fungal hyphae treated with AgNPs. Disturbances in the cell walls and membranes, as well as empty space in the cytoplasm were observed. The transcriptome sequencing of F. solani species complex mycelia was performed using the Illumina NextSeq 500 ribonucleic acid sequencing (RNA-Seq) platform. In the RNA-Seq study, AgNPs treatment resulted in 2503 differentially expressed genes (DEGs). Gene Ontology (GO) analysis revealed that the DEGs were mainly involved in 6 different terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis also revealed that energy and substance metabolism, signal transduction and genetic information processing were the most highly enriched pathways for these DEGs. In addition, RNA-seq results were validated by quantitative polymerase chain reactions (qPCRs). Our findings enhanced the understanding of the antifungal activities of AgNPs and the underlying molecular mechanisms, and provided a new perspective for investigating this novel antifungal agent.
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Affiliation(s)
- Tianlin Shen
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Qiushuang Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Chengliang Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuhuan Li
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yanli Liu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, State Key Laboratory of Nutrition Resources Integrated Utilization, College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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22
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Achari SR, Kaur J, Dinh Q, Mann R, Sawbridge T, Summerell BA, Edwards J. Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model. BMC Genomics 2020; 21:248. [PMID: 32197583 PMCID: PMC7085163 DOI: 10.1186/s12864-020-6640-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/03/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic relatedness within the complex has been studied by sequencing either the genes or the barcoding gene regions within those genes. Phylogenetic analyses have demonstrated a great deal of diversity which is reflected in the differing number of clades identified: three, five and eight. Genetic limitation within the species in the complex has been studied through Genealogical Concordance Phylogenetic Species Recognition (GCPSR) analyses with varying number of phylogenetic 'species' identified ranging from two to 21. Such differing views have continued to confuse users of these taxonomies. RESULTS The phylogenetic relationships between Australian F. oxysporum isolates from both natural and agricultural ecosystems were determined using three datasets: whole genome, nuclear genes, and mitochondrial genome sequences. The phylogenies were concordant except for three isolates. There were three concordant clades from all the phylogenies suggesting similar evolutionary history for mitochondrial genome and nuclear genes for the isolates in these three clades. Applying a multispecies coalescent (MSC) model on the eight single copy nuclear protein coding genes from the nuclear gene dataset concluded that the three concordant clades correspond to three phylogenetic species within the FOSC. There was 100% posterior probability support for the formation of three species within the FOSC. This is the first report of using the MSC model to estimate species within the F. oxysporum species complex. The findings from this study were compared with previously published phylogenetics and species delimitation studies. CONCLUSION Phylogenetic analyses using three different gene datasets from Australian F. oxysporum isolates have all supported the formation of three major clades which delineated into three species. Species 2 (Clade 3) may be called F. oxysporum as it contains the neotype for F. oxysporum.
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Affiliation(s)
- Saidi R Achari
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, Australia.
- La Trobe University, Victoria, Australia.
| | - Jatinder Kaur
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, Australia
| | - Quang Dinh
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, Australia
| | - Ross Mann
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, Australia
| | - Tim Sawbridge
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, Australia
- La Trobe University, Victoria, Australia
| | - Brett A Summerell
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | - Jacqueline Edwards
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, Australia
- La Trobe University, Victoria, Australia
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23
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Liu W, Cai Y, Zhang Q, Chen L, Shu F, Ma X, Bian Y. The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences. Int J Biol Macromol 2019; 143:373-381. [PMID: 31830457 DOI: 10.1016/j.ijbiomac.2019.12.056] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 12/11/2022]
Abstract
The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.
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Affiliation(s)
- Wei Liu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingli Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Qianqian Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Shu
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan 430070, China.
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24
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Park J, Kwon W, Kim JB, Park MJ, Kim TS. Complete mitochondrial genome sequence of lettuce pathogenic fungus, Fusarium oxysporum f. sp. lactucae 09-002. Mitochondrial DNA B Resour 2019; 4:3434-3436. [PMID: 33366027 PMCID: PMC7706453 DOI: 10.1080/23802359.2019.1667902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022] Open
Abstract
Fusarium oxysporum is a famous plant pathogenic filamentous fungus. Here, we report the complete mitochondrial genome sequence of F. oxysporum f. sp. lactucae isolated from the lettuce field in Suwon area, Korea. Total length of the mitochondrial genome is 45,020 bp and it encodes 42 genes (15 protein-coding genes, two rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 32.7%, and overall GC content is 32.4%. Phylogenetic tree presented that F. oxysporum f. sp. lactucae 09-002 was clustered with Fusarium commune not like another F. oxysporum mitochondrial genomes, requiring further analyses.
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Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Woochan Kwon
- Infoboss Co., Ltd., Seoul, Korea
- InfoBoss Research Center, Seoul, Korea
| | - Jung-Bun Kim
- Department of Agriculture and Life Sciences, Korea National Open University, Seoul, Korea
| | - Mi-Jeong Park
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Korea
| | - Tae-Sung Kim
- Department of Agriculture and Life Sciences, Korea National Open University, Seoul, Korea
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25
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Nielsen MR, Sondergaard TE, Giese H, Sørensen JL. Advances in linking polyketides and non-ribosomal peptides to their biosynthetic gene clusters in Fusarium. Curr Genet 2019; 65:1263-1280. [DOI: 10.1007/s00294-019-00998-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/24/2022]
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26
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Kolesnikova AI, Putintseva YA, Simonov EP, Biriukov VV, Oreshkova NV, Pavlov IN, Sharov VV, Kuzmin DA, Anderson JB, Krutovsky KV. Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species. BMC Genomics 2019; 20:351. [PMID: 31068137 PMCID: PMC6506933 DOI: 10.1186/s12864-019-5732-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/24/2019] [Indexed: 12/03/2022] Open
Abstract
Background Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time. Results Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes. Conclusions Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5732-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna I Kolesnikova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia
| | - Yuliya A Putintseva
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia
| | - Evgeniy P Simonov
- Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Institute of Animal Systematics and Ecology, Siberian Branch of Russian Academy of Sciences, 630091, Novosibirsk, Russia
| | - Vladislav V Biriukov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia
| | - Natalya V Oreshkova
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Igor N Pavlov
- Laboratory of Reforestation, Mycology and Plant Pathology, V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia
| | - Vadim V Sharov
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Laboratory of Genomic Research and Biotechnology, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russia.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - Dmitry A Kuzmin
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia.,Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russia
| | - James B Anderson
- Department of Biology, University of Toronto, Mississauga, ON, l5L 1C6, Canada
| | - Konstantin V Krutovsky
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russia. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany. .,Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia. .,Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, 77843-2138, USA.
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27
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Zhou X, Cao ZM, Liu X, Kim HS, Proctor RH, O'Donnell K. Maternal mitochondrial inheritance in two Fusarium pathogens of prickly ash (Zanthoxylum bungeanum) in northern China. Mycologia 2019; 111:235-243. [PMID: 30896371 DOI: 10.1080/00275514.2018.1562269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mitochondrial inheritance in Fusarium zanthoxyli and F. continuum, two canker-inducing pathogens of prickly ash (Zanthoxylum bungeanum) in northern China, was investigated by genotyping ascospore progeny obtained from laboratory crosses. Polymorphic regions of the mitochondrial genomes (mitogenomes) that contained indels and single-nucleotide polymorphisms (SNPs) were identified via comparative analyses of the complete mitogenomes of the parents used in the intraspecific crosses. A reciprocal genetic cross of F. zanthoxyli NRRL 66714 × NRRL 66285, and a separate cross of F. continuum ♀ NRRL 66286 × ♂ NRRL 66218, revealed that mitochondria were only inherited from the maternal parent. In addition, the reciprocal cross demonstrated that mitochondrial inheritance is not linked to mating type. Gene order in the circular mitogenomes of the prickly ash pathogens was identical to that previously reported for other fusaria and members of the Hypocreales, except that the TRNL tRNAs were duplicated in F. zanthoxyli NRRL 66714. The genomes contained 14 polypeptide-encoding genes involved in oxidative respiration, one intron-encoded ribosomal protein (rps3) gene, two ribosomal RNA (rRNA) genes, and 26-28 tRNA genes. The F. zanthoxyli mitogenomes were 80.9 and 98.7 kb in length, whereas those of F. continuum were considerably shorter and nearly identical in length at 63.4 kb. The significant differences in mitogenome length were primarily due to variable numbers of introns and open reading frames (ORFs) encoding hypothetical proteins.
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Affiliation(s)
- Xue Zhou
- a College of Forestry, Northwest A&F University , Taicheng Road, Yangling , Shaanxi 712100 , China
| | - Zhi-Min Cao
- a College of Forestry, Northwest A&F University , Taicheng Road, Yangling , Shaanxi 712100 , China
| | - Xin Liu
- a College of Forestry, Northwest A&F University , Taicheng Road, Yangling , Shaanxi 712100 , China
| | - Hye-Seon Kim
- b Mycotoxin Prevention and Applied Microbiology (MPM) Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service , US Department of Agriculture , Peoria , Illinois 60604-3999
| | - Robert H Proctor
- b Mycotoxin Prevention and Applied Microbiology (MPM) Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service , US Department of Agriculture , Peoria , Illinois 60604-3999
| | - Kerry O'Donnell
- b Mycotoxin Prevention and Applied Microbiology (MPM) Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service , US Department of Agriculture , Peoria , Illinois 60604-3999
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28
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Brankovics B, Kulik T, Sawicki J, Bilska K, Zhang H, de Hoog GS, van der Lee TA, Waalwijk C, van Diepeningen AD. First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes. PeerJ 2018; 6:e5963. [PMID: 30588394 PMCID: PMC6304159 DOI: 10.7717/peerj.5963] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/16/2018] [Indexed: 01/13/2023] Open
Abstract
There is a gradual shift from representing a species' genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The "intronless" mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the "host" gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.
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Affiliation(s)
- Balázs Brankovics
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, P.R. China
| | - G Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Theo Aj van der Lee
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Anne D van Diepeningen
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands.,Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
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29
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Li Q, Liao M, Yang M, Xiong C, Jin X, Chen Z, Huang W. Characterization of the mitochondrial genomes of three species in the ectomycorrhizal genus Cantharellus and phylogeny of Agaricomycetes. Int J Biol Macromol 2018; 118:756-769. [DOI: 10.1016/j.ijbiomac.2018.06.129] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022]
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30
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Fungal mitochondrial genomes and genetic polymorphisms. Appl Microbiol Biotechnol 2018; 102:9433-9448. [PMID: 30209549 DOI: 10.1007/s00253-018-9350-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/24/2022]
Abstract
Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.
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31
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Deng Y, Hsiang T, Li S, Lin L, Wang Q, Chen Q, Xie B, Ming R. Comparison of the Mitochondrial Genome Sequences of Six Annulohypoxylon stygium Isolates Suggests Short Fragment Insertions as a Potential Factor Leading to Larger Genomic Size. Front Microbiol 2018; 9:2079. [PMID: 30250455 PMCID: PMC6140425 DOI: 10.3389/fmicb.2018.02079] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in the eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium (Lév.) were assembled from raw reads from PacBio and Illumina sequencing. The diversity of genomic structures, conserved genes, intergenic regions and introns were analyzed and compared. Genome sizes ranged from 132 to 147 kb and contained the same sets of conserved protein-coding, tRNA and rRNA genes and shared the same gene arrangements and orientation. In addition, most intergenic regions were homogeneous and had similar sizes except for the region between cytochrome b (cob) and cytochrome c oxidase I (cox1) genes which ranged from 2,998 to 8,039 bp among the six isolates. Sixty-five intron insertion sites and 99 different introns were detected in these genomes. Each genome contained 45 or more introns, which varied in distribution and content. Introns from homologous insertion sites also showed high diversity in size, type and content. Comparison of introns at the same loci showed some complex introns, such as twintrons and ORF-less introns. There were 44 short fragment insertions detected within introns, intergenic regions, or as introns, some of them located at conserved domain regions of homing endonuclease genes. Insertions of short fragments such as small inverted repeats might affect or hinder the movement of introns, and these allowed for intron accumulation in the mitochondrial genomes analyzed, and enlarged their size. This study showed that the evolution of fungal mitochondrial introns is complex, and the results suggest short fragment insertions as a potential factor leading to larger mitochondrial genomes in A. stygium.
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Affiliation(s)
- Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Tom Hsiang
- Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Shuxian Li
- USDA-Agricultural Research Service, Crop Genetics Research Unit, Stoneville, MS, United States
| | - Longji Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingfu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinghe Chen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Baogui Xie
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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32
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Rivera Y, Salgado-Salazar C, Veltri D, Malapi-Wight M, Crouch JA. Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola. PeerJ 2018; 6:e5401. [PMID: 30155349 PMCID: PMC6110257 DOI: 10.7717/peerj.5401] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/18/2018] [Indexed: 01/15/2023] Open
Abstract
Boxwood (Buxus spp.) are broad-leaved, evergreen landscape plants valued for their longevity and ornamental qualities. Volutella leaf and stem blight, caused by the ascomycete fungi Pseudonectria foliicola and P. buxi, is one of the major diseases affecting the health and ornamental qualities of boxwood. Although this disease is less severe than boxwood blight caused by Calonectria pseudonaviculata and C. henricotiae, its widespread occurrence and disfiguring symptoms have caused substantial economic losses to the ornamental industry. In this study, we sequenced the genome of P. foliicola isolate ATCC13545 using Illumina technology and compared it to other publicly available fungal pathogen genomes to better understand the biology of this organism. A de novo assembly estimated the genome size of P. foliicola at 28.7 Mb (425 contigs; N50 = 184,987 bp; avg. coverage 188×), with just 9,272 protein-coding genes. To our knowledge, P. foliicola has the smallest known genome within the Nectriaceae. Consistent with the small size of the genome, the secretome, CAzyme and secondary metabolite profiles of this fungus are reduced relative to two other surveyed Nectriaceae fungal genomes: Dactylonectria macrodidyma JAC15-245 and Fusarium graminearum Ph-1. Interestingly, a large cohort of genes associated with reduced virulence and loss of pathogenicity was identified from the P. foliicola dataset. These data are consistent with the latest observations by plant pathologists that P. buxi and most likely P. foliicola, are opportunistic, latent pathogens that prey upon weak and stressed boxwood plants.
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Affiliation(s)
- Yazmín Rivera
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
- Current affiliation: Center for Plant Health, Science and Technology, USDA, Animal and Plant Health Inspection Service, Beltsville, MD, United States of America
| | - Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Daniel Veltri
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
- Current affiliation: Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America
| | - Martha Malapi-Wight
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- Current affiliation: Plant Germplasm Quarantine Program, USDA, Animal and Plant Health Inspection Service, Beltsville, MD, United States of America
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
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33
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Hoogendoorn K, Barra L, Waalwijk C, Dickschat JS, van der Lee TAJ, Medema MH. Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium. Front Microbiol 2018; 9:1158. [PMID: 29922257 PMCID: PMC5996196 DOI: 10.3389/fmicb.2018.01158] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium, to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus. Comparison with MIBiG reference BGCs allowed assignment of 29 gene cluster families (GCFs) to pathways responsible for the production of known compounds, while for 57 GCFs, the molecular products remain unknown. Comparative analysis of BGC repertoires using ancestral state reconstruction raised several new hypotheses on how BGCs contribute to Fusarium pathogenicity or host specificity, sometimes surprisingly so: for example, a gene cluster for the biosynthesis of hexadehydro-astechrome was identified in the genome of the biocontrol strain Fusarium oxysporum Fo47, while being absent in that of the tomato pathogen F. oxysporum f.sp. lycopersici. Several BGCs were also identified on supernumerary chromosomes; heterologous expression of genes for three terpene synthases encoded on the Fusarium poae supernumerary chromosome and subsequent GC/MS analysis showed that these genes are functional and encode enzymes that each are able to synthesize koraiol; this observed functional redundancy supports the hypothesis that localization of copies of BGCs on supernumerary chromosomes provides freedom for evolutionary innovations to occur, while the original function remains conserved. Altogether, this systematic overview of biosynthetic diversity in Fusarium paves the way for targeted natural product discovery based on automated identification of species-specific pathways as well as for connecting species ecology to the taxonomic distributions of BGCs.
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Affiliation(s)
- Koen Hoogendoorn
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands.,Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Lena Barra
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Cees Waalwijk
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
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34
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Fourie G, Van der Merwe NA, Wingfield BD, Bogale M, Wingfield MJ, Steenkamp ET. Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex. IMA Fungus 2018; 9:37-48. [PMID: 30018871 PMCID: PMC6048563 DOI: 10.5598/imafungus.2018.09.01.04] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/18/2018] [Indexed: 01/31/2023] Open
Abstract
The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.
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Affiliation(s)
- Gerda Fourie
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicolaas A Van der Merwe
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Mesfin Bogale
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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35
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de Queiroz CB, Santana MF, Pereira Vidigal PM, de Queiroz MV. Comparative analysis of the mitochondrial genome of the fungus Colletotrichum lindemuthianum, the causal agent of anthracnose in common beans. Appl Microbiol Biotechnol 2018; 102:2763-2778. [PMID: 29453633 DOI: 10.1007/s00253-018-8812-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 01/25/2023]
Abstract
Fungi of the genus Colletotrichum are economically important and are used as models in plant-pathogen interaction studies. In this study, the complete mitochondrial genomes of two Colletotrichum lindemuthianum isolates were sequenced and compared with the mitochondrial genomes of seven species of Colletotrichum. The mitochondrial genome of C. lindemuthianum is a typical circular molecule 37,446 bp (isolate 89 A2 2-3) and 37,440 bp (isolate 83.501) in length. The difference of six nucleotides between the two genomes is the result of a deletion in the ribosomal protein S3 (rps3) gene in the 83.501 isolate. In addition, substitution of adenine for guanine within the rps3 gene in the mitochondrial genome of the 83.501 isolate was observed. Compared to the previously sequenced C. lindemuthianum mitochondrial genome, an exon no annotated in the cytochrome c oxidase I (cox1) gene and a non-conserved open reading frame (ncORF) were observed. The size of the mitochondrial genomes of the seven species of Colletotrichum was highly variable, being attributed mainly to the ncORF, ranging from one to 10 and also from introns ranging from one to 11 and which encode a total of up to nine homing endonucleases. This paper reports for the first time by means of transcriptome that then ncORFs are transcribed in Colletotrichum spp. Phylogeny data revealed that core mitochondrial genes could be used as an alternative in phylogenetic relationship studies in Colletotrichum spp. This work contributes to the genetic and biological knowledge of Colletotrichum spp., which is of great economic and scientific importance.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Genética Molecular de Fungos (LGMF)/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, CEP: 36570-900, Brazil
| | - Mateus Ferreira Santana
- Laboratório de Genética Molecular de Fungos (LGMF)/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, CEP: 36570-900, Brazil
| | - Pedro M Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Centro de Ciências Biológicas, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marisa Vieira de Queiroz
- Laboratório de Genética Molecular de Fungos (LGMF)/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, CEP: 36570-900, Brazil.
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36
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Zeng L, Liu C, Lin R, Kang X, Xie B, Xiong X. Complete mitogenome of the high ethanol production fungus Fusarium oxysporum Mh2-2. Mitochondrial DNA B Resour 2017; 2:814-815. [PMID: 33473993 PMCID: PMC7799908 DOI: 10.1080/23802359.2017.1398601] [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] [Indexed: 11/18/2022] Open
Abstract
Fusarium spp. are significantly important plant pathogens, and some of them are ethanol-producing strains. During infection and/or ethanol production, Fusarium requires a plenty of energy that is mainly provided by mitochondria. Here we report the first mitogenome from a selected Fusarium oxysporum strain mh2-2 that produces ethanol from glucose and xylose. The size of this mitogenome, 46 kb, is different from the size of any reported Fusarium mitogenome. Our results provide insight into the functions and evolution of mitochondrial genes and genomes.
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Affiliation(s)
- Lu Zeng
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, Hunan, China
| | - Chichuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xincong Kang
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, Hunan, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingyao Xiong
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, Hunan, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Brankovics B, van Dam P, Rep M, de Hoog GS, J. van der Lee TA, Waalwijk C, van Diepeningen AD. Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex. BMC Genomics 2017; 18:735. [PMID: 28923029 PMCID: PMC5604515 DOI: 10.1186/s12864-017-4116-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 09/05/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. RESULTS A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. CONCLUSIONS The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.
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Affiliation(s)
- Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - Peter van Dam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - Martijn Rep
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH The Netherlands
| | - Theo A. J. van der Lee
- Wageningen University and Research Centre, Droevendaalsesteeg 4, Wageningen, 6708 PB The Netherlands
| | - Cees Waalwijk
- Wageningen University and Research Centre, Droevendaalsesteeg 4, Wageningen, 6708 PB The Netherlands
| | - Anne D. van Diepeningen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584CT The Netherlands
- Wageningen University and Research Centre, Droevendaalsesteeg 4, Wageningen, 6708 PB The Netherlands
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Zaccaron AZ, Woloshuk CP, Bluhm BH. Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis. Fungal Biol 2017; 121:966-983. [PMID: 29029703 DOI: 10.1016/j.funbio.2017.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 12/11/2022]
Abstract
Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S. maydis. Analyses of predicted genes involved in starch degradation revealed six putative α-amylases, four extracellular and two intracellular, and two putative γ-amylases, one of which appears to have been acquired from bacteria via horizontal transfer. Additionally, 87 backbone genes involved in secondary metabolism were identified, which represents one of the largest known assemblages among Pezizomycotina species. Numerous secondary metabolite gene clusters were identified, including two clusters likely involved in the biosynthesis of diplodiatoxin and chaetoglobosins. The draft genome of S. maydis presented here will serve as a useful resource for molecular genetics, functional genomics, and analyses of population diversity in this organism.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, AR 72701, USA
| | - Charles P Woloshuk
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Burton H Bluhm
- Department of Plant Pathology, University of Arkansas, Division of Agriculture, Fayetteville, AR 72701, USA.
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Liang X, Tian X, Liu W, Wei T, Wang W, Dong Q, Wang B, Meng Y, Zhang R, Gleason ML, Sun G. Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato: insights into the evolution of a fungal species complex interacting with diverse plants. BMC Genomics 2017; 18:171. [PMID: 28201983 PMCID: PMC5311727 DOI: 10.1186/s12864-016-3480-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology. In this study, we first sequenced and compared nine mitogenomes belonging to four C. gloeosporioides s.l. species lineages (C. gloeosporioides, C. fructicola, C. aenigma, and C. siamense s.l.), and evaluated the usefulness of mitogenome sequence in complementing prevailing nuclear markers for species delimitation. RESULTS The C. gloeosporioides s.l. mitogenomes ranged between 52,671 and 58,666 bp in size, and each contained an identical set of genes transcribed in the same direction. Compared with previously reported Colletotrichum mitogenomes, these mitogenomes were uniquely featured by: (1) significantly larger genome size due to richer intron content and longer intergenic region; (2) striking GC content elevation at the intergenic region; and (3) considerable intron content variation among different species lineages. Compared with nuclear DNA markers commonly used in phylogeny, the mitogenome nucleotide diversity was extremely low, yet the mitogenome alignment contained the highest number of parsimony informative sites, which allowed the generation of a high-resolution phylogeny recognizing all taxonomic lineages, including ones belonging to the very nascent C. siamense s.l. complex. The tree topology was highly congruent with the phylogeny based on nuclear marker concatenation except for lineages within C. siamense s.l. Further comparative phylogenetic analysis indicated that lineage-specific rapid divergence of GS and SOD2 markers confounded concatenation-based species relationship inference. CONCLUSIONS This study sheds light on the evolution of C. gloeosporioides s.l. mitogenomes and demonstrates that mitogenome sequence can complement prevailing nuclear markers in improving species delimitation accuracy. The mitogenome sequences reported will be valuable resources for further genetic studies with C. gloeosporioides s.l. and other Colletotrichum species.
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Affiliation(s)
- Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Xianglin Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Wenkui Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Tingyu Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Qiuyue Dong
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Yanan Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Mark L. Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
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Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species. PLoS One 2016; 11:e0156104. [PMID: 27272523 PMCID: PMC4894602 DOI: 10.1371/journal.pone.0156104] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/08/2016] [Indexed: 01/21/2023] Open
Abstract
In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.
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Jelen V, de Jonge R, Van de Peer Y, Javornik B, Jakše J. Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae. PLoS One 2016; 11:e0148525. [PMID: 26839950 PMCID: PMC4739603 DOI: 10.1371/journal.pone.0148525] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/20/2016] [Indexed: 01/04/2023] Open
Abstract
Verticillium nonalfalfae is a fungal plant pathogen that causes wilt disease by colonizing the vascular tissues of host plants. The disease induced by hop isolates of V. nonalfalfae manifests in two different forms, ranging from mild symptoms to complete plant dieback, caused by mild and lethal pathotypes, respectively. Pathogenicity variations between the causal strains have been attributed to differences in genomic sequences and perhaps also to differences in their mitochondrial genomes. We used data from our recent Illumina NGS-based project of genome sequencing V. nonalfalfae to study the mitochondrial genomes of its different strains. The aim of the research was to prepare a V. nonalfalfae reference mitochondrial genome and to determine its phylogenetic placement in the fungal kingdom. The resulting 26,139 bp circular DNA molecule contains a full complement of the 14 "standard" fungal mitochondrial protein-coding genes of the electron transport chain and ATP synthase subunits, together with a small rRNA subunit, a large rRNA subunit, which contains ribosomal protein S3 encoded within a type IA-intron and 26 tRNAs. Phylogenetic analysis of this mitochondrial genome placed it in the Verticillium spp. lineage in the Glomerellales group, which is also supported by previous phylogenetic studies based on nuclear markers. The clustering with the closely related Verticillium dahliae mitochondrial genome showed a very conserved synteny and a high sequence similarity. Two distinguishing mitochondrial genome features were also found-a potential long non-coding RNA (orf414) contained only in the Verticillium spp. of the fungal kingdom, and a specific fragment length polymorphism observed only in V. dahliae and V. nubilum of all the Verticillium spp., thus showing potential as a species specific biomarker.
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Affiliation(s)
- Vid Jelen
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ronnie de Jonge
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Gent University, Gent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Gent University, Gent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Branka Javornik
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Coleman JJ. The Fusarium solani species complex: ubiquitous pathogens of agricultural importance. MOLECULAR PLANT PATHOLOGY 2016; 17:146-58. [PMID: 26531837 PMCID: PMC6638333 DOI: 10.1111/mpp.12289] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
UNLABELLED Members of the Fusarium solani species complex (FSSC) are capable of causing disease in many agriculturally important crops. The genomes of some of these fungi include supernumerary chromosomes that are dispensable and encode host-specific virulence factors. In addition to genomics, this review summarizes the known molecular mechanisms utilized by members of the FSSC in establishing disease. TAXONOMY Kingdom Fungi; Phylum Ascomycota; Class Sordariomycetes; Order Hypocreales; Family Nectriaceae; Genus Fusarium. HOST RANGE Members of the FSSC collectively have a very broad host range, and have been subdivided previously into formae speciales. Recent phylogenetic analysis has revealed that formae speciales correspond to biologically and phylogenetically distinct species. DISEASE SYMPTOMS Typically, FSSC causes foot and/or root rot of the infected host plant, and the degree of necrosis correlates with the severity of the disease. Symptoms on above-ground portions of the plant can vary greatly depending on the specific FSSC pathogen and host plant, and the disease may manifest as wilting, stunting and chlorosis or lesions on the stem and/or leaves. CONTROL Implementation of agricultural management practices, such as crop rotation and timing of planting, can reduce the risk of crop loss caused by FSSC. If available, the use of resistant varieties is another means to control disease in the field. USEFUL WEBSITES http://genome.jgi-psf.org/Necha2/Necha2.home.html.
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Affiliation(s)
- Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
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Konovalova O, Logacheva M. Mitochondrial genome of two marine fungal species. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4280-4281. [DOI: 10.3109/19401736.2015.1082094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Olga Konovalova
- White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia and
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Gong L, Jiang Y, Chen F. Molecular strategies for detection and quantification of mycotoxin-producing Fusarium species: a review. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:1767-1776. [PMID: 25255897 DOI: 10.1002/jsfa.6935] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/19/2014] [Accepted: 09/19/2014] [Indexed: 06/03/2023]
Abstract
Fusarium contamination is considered a major agricultural problem, which could not only significantly reduce yield and quality of agricultural products, but produce mycotoxins that are virulence factors responsible for many diseases of humans and farm animals. One strategy to identify toxigenic Fusarium species is the use of modern molecular methods, which include the analysis of DNA target regions for differentiation of the Fusarium species, particularly the mycotoxin-producing Fusarium species such as F. verticillioides and F. graminearum. Additionally, polymerase chain reaction assays are used to determine the genes involved in the biosynthesis of the toxins in order to facilitate a qualitative and quantitative detection of Fusarium-producing mycotoxins. Also, it is worth mentioning that some factors that modulate the biosynthesis of mycotoxins are not only determined by their biosynthetic gene clusters, but also by environmental conditions. Therefore, all of the aforementioned factors which may affect the molecular diagnosis of mycotoxins will be reviewed and discussed in this paper.
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Affiliation(s)
- Liang Gong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong Province, China
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong Province, China
| | - Feng Chen
- Department of Food, Nutrition and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
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Lin R, Liu C, Shen B, Bai M, Ling J, Chen G, Mao Z, Cheng X, Xie B. Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales. BMC Microbiol 2015; 15:5. [PMID: 25636983 PMCID: PMC4360972 DOI: 10.1186/s12866-015-0341-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 01/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales. Results The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae. Conclusions We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0341-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chichuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Baoming Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Miao Bai
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guohua Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xinyue Cheng
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Aguileta G, de Vienne DM, Ross ON, Hood ME, Giraud T, Petit E, Gabaldón T. High variability of mitochondrial gene order among fungi. Genome Biol Evol 2015; 6:451-65. [PMID: 24504088 PMCID: PMC3942027 DOI: 10.1093/gbe/evu028] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we analyzed 38 complete fungal mt genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We investigated the effect that introns, intronic open reading frames (ORFs), and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mt genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns, and associated ORFs. Our results support previous evidence for the presence of mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.
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Affiliation(s)
- Gabriela Aguileta
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
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Lysøe E, Harris LJ, Walkowiak S, Subramaniam R, Divon HH, Riiser ES, Llorens C, Gabaldón T, Kistler HC, Jonkers W, Kolseth AK, Nielsen KF, Thrane U, Frandsen RJN. The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism. PLoS One 2014; 9:e112703. [PMID: 25409087 PMCID: PMC4237347 DOI: 10.1371/journal.pone.0112703] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/13/2014] [Indexed: 12/03/2022] Open
Abstract
Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.
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Affiliation(s)
- Erik Lysøe
- Department of Plant Health and Plant Protection, Bioforsk - Norwegian Institute of Agricultural and Environmental Research, Ås, Norway
- * E-mail:
| | - Linda J. Harris
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Sean Walkowiak
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
- Department of Biology, Carleton University, Ottawa, Canada
| | - Rajagopal Subramaniam
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
- Department of Biology, Carleton University, Ottawa, Canada
| | - Hege H. Divon
- Section of Mycology, Norwegian Veterinary Institute, Oslo, Norway
| | - Even S. Riiser
- Department of Plant Health and Plant Protection, Bioforsk - Norwegian Institute of Agricultural and Environmental Research, Ås, Norway
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - H. Corby Kistler
- ARS-USDA, Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Wilfried Jonkers
- ARS-USDA, Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Anna-Karin Kolseth
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kristian F. Nielsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ulf Thrane
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes. Curr Genet 2014; 60:303-13. [PMID: 25011705 PMCID: PMC4201751 DOI: 10.1007/s00294-014-0436-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 05/30/2014] [Accepted: 06/21/2014] [Indexed: 01/13/2023]
Abstract
Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.
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Terzi V, Tumino G, Stanca AM, Morcia C. Reducing the incidence of cereal head infection and mycotoxins in small grain cereal species. J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2013.10.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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50
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Torriani SF, Penselin D, Knogge W, Felder M, Taudien S, Platzer M, McDonald BA, Brunner PC. Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion. Fungal Genet Biol 2014; 62:34-42. [DOI: 10.1016/j.fgb.2013.11.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/08/2013] [Accepted: 11/01/2013] [Indexed: 01/07/2023]
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