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Deng Y, Chen G, Bao X, He J, Li Q. Characterization of the complete mitochondrial genome of Mucor indicus Lendn. 1930 (Mucorales: Mucoraceae), isolated from the wine fermentation system. Mitochondrial DNA B Resour 2024; 9:845-849. [PMID: 38939449 PMCID: PMC11210418 DOI: 10.1080/23802359.2024.2371376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
Mucor indicus Lendn. 1930 has been widely used in food fermentation; however, its mitochondrial genome characteristics are not well understood. In this study, the complete mitochondrial genome of M. indicus was obtained, which was 61,400 bp in length with a GC content of 33%. The M. indicus mitochondrial genome was found to contain 14 core protein-coding genes, four free-standing ORFs, 18 intronic ORFs, 26 tRNAs, and two rRNA genes. Phylogenetic trees were generated for 25 early-differentiated fungi using the Bayesian inference (BI) method, which demonstrated that M. indicus is closely related to Mucor piriformis. This study provides useful information for the classification and evolution of Mucor species or other early-differentiated fungi.
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Affiliation(s)
- Yue Deng
- Luzhou Vocational and Technical College, Luzhou, P. R. China
| | - Guangjiu Chen
- Luzhou Vocational and Technical College, Luzhou, P. R. China
| | - Xuedong Bao
- Luzhou Vocational and Technical College, Luzhou, P. R. China
| | - Jie He
- Luzhou Vocational and Technical College, Luzhou, P. R. China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, P. R. China
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Deng Y, Chen G, Bao X, He J, Li Q. Mitochondrial genomic characteristics and phylogenetic analysis of a brewing fungus, Rhizopus microsporus Tiegh. 1875 (Mucorales: Rhizopodaceae). Mitochondrial DNA B Resour 2024; 9:657-662. [PMID: 38774188 PMCID: PMC11107855 DOI: 10.1080/23802359.2024.2356133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/12/2024] [Indexed: 05/24/2024] Open
Abstract
Rhizopus microsporus Tiegh. 1875 is widely used in a variety of industries, such as brewing, wine making, baking, and medicine production, as it has the capability to break down proteins and generate surface-active agents. To date, the mitochondrial genome features of early evolved fungi from the Rhizopus genus have not been extensively studied. Our research obtained a full mitochondrial genome of R. microsporus species, which was 43,837 bp in size and had a GC content of 24.93%. This genome contained 14 core protein-coding genes, 3 independent ORFs, 7 intronic ORFs, 24 tRNAs, and 2 rRNA genes. Through the use of the BI phylogenetic inference method, we were able to create phylogenetic trees for 25 early differentiation fungi which strongly supported the major clades; this indicated that R. microsporus is most closely related to Rhizopus oryzae.
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Affiliation(s)
- Yue Deng
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Guangjiu Chen
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Xuedong Bao
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Jie He
- Luzhou Vocational and Technical College, Luzhou, Sichuan, P. R. China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, P. R. China
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Yurkov AP, Kryukov AA, Gorbunova AO, Kudriashova TR, Kovalchuk AI, Gorenkova AI, Bogdanova EM, Laktionov YV, Zhurbenko PM, Mikhaylova YV, Puzanskiy RK, Bagrova TN, Yakhin OI, Rodionov AV, Shishova MF. Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot. J Fungi (Basel) 2023; 10:11. [PMID: 38248921 PMCID: PMC10817546 DOI: 10.3390/jof10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes. METHODS The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references. RESULTS We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively. CONCLUSION High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.
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Affiliation(s)
- Andrey P. Yurkov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Alexey A. Kryukov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Anastasiia O. Gorbunova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Tatyana R. Kudriashova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Kovalchuk
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Graduate School of Biotechnology and Food Science, Peter the Great St. Petersburg Polytechnic University, 194064 St. Petersburg, Russia
| | - Anastasia I. Gorenkova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ekaterina M. Bogdanova
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Yuri V. Laktionov
- Laboratory of Ecology of Symbiotic and Associative Rhizobacteria, All-Russia Research Institute for Agricultural Microbiology, Pushkin, 196608 St. Petersburg, Russia; (A.A.K.); (A.O.G.); (T.R.K.); (A.I.K.); (A.I.G.); (E.M.B.); (Y.V.L.)
| | - Peter M. Zhurbenko
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Roman K. Puzanskiy
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia;
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Tatyana N. Bagrova
- Faculty of Ecology, Russian State Hydrometeorological University, 192007 St. Petersburg, Russia;
| | - Oleg I. Yakhin
- Institute of Biochemistry and Genetics, The Ufa Federal Research Center of the Russian Academy of Sciences, 450054 Ufa, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197022 St. Petersburg, Russia; (P.M.Z.); (Y.V.M.); (A.V.R.)
| | - Maria F. Shishova
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
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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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Fatma T, Ahmed Khan H, Ahmed A, Adnan F, Zeshan, Virk N, Faraz Bhatti M. Functional annotation and comparative analysis of four Botrytis cinerea mitogenomes reported from Punjab, Pakistan. Saudi J Biol Sci 2023; 30:103605. [PMID: 36950365 PMCID: PMC10025148 DOI: 10.1016/j.sjbs.2023.103605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/02/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Botrytis cinerea is one of the top phytopathogenic fungus which ubiquitously cause grey mold on a variety of horticultural plants. The mechanism of respiration in the fungus occurs within the mitochondria. Mitogenomes serve as a key molecular marker for the investigation of fungal evolutionary patterns. This study aimed at the complete assembly, characterization, and comparative relationship of four mitogenomes of Botrytis cinerea strains including Kst5C, Kst14A, Kst32B, Kst33A, respectively. High throughput sequencing of four mitogenomes allowed the full assembly and annotation of these sequences. The total genome length of these 4 isolates Kst5C Kst14A, Kst32B, Kst33A was 69,986 bp, 77,303 bp, 76,204 bp and 55, 226 bp respectively. The distribution of features represented 2 ribosomal RNA genes,14 respiration encoding proteins, 1 mitochondrial ribosomal protein-encoding gene, along with varying numbers of transfer RNA genes, protein-coding genes, mobile intronic regions and homing endonuclease genes including LAGLIDADG and GIY-YIG domains were found in all four mitogenomes. The comparative analyses performed also decipher significant results for four mitogenomes among fungal isolates included in the study. This is the first report on the detailed annotation of mitogenomes as a proof for investigation of variation patterns present with in the B. cinerea causing grey mold on strawberries in Pakistan. This study will also contribute to the rapid evolutionary analysis and population patterns present among Botrytis cinerea.
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Affiliation(s)
- Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Zeshan
- Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
- Corresponding author.
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6
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The Potential Applications of Commercial Arbuscular Mycorrhizal Fungal Inoculants and Their Ecological Consequences. Microorganisms 2022; 10:microorganisms10101897. [PMID: 36296173 PMCID: PMC9609176 DOI: 10.3390/microorganisms10101897] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/18/2022] Open
Abstract
Arbuscular mycorrhizal fungal (AMF) inoculants are sustainable biological materials that can provide several benefits to plants, especially in disturbed agroecosystems and in the context of phytomanagement interventions. However, it is difficult to predict the effectiveness of AMF inoculants and their impacts on indigenous AMF communities under field conditions. In this review, we examined the literature on the possible outcomes following the introduction of AMF-based inoculants in the field, including their establishment in soil and plant roots, persistence, and effects on the indigenous AMF community. Most studies indicate that introduced AMF can persist in the target field from a few months to several years but with declining abundance (60%) or complete exclusion (30%). Further analysis shows that AMF inoculation exerts both positive and negative impacts on native AMF species, including suppression (33%), stimulation (38%), exclusion (19%), and neutral impacts (10% of examined cases). The factors influencing the ecological fates of AMF inoculants, such as the inherent properties of the inoculum, dosage and frequency of inoculation, and soil physical and biological factors, are further discussed. While it is important to monitor the success and downstream impacts of commercial inoculants in the field, the sampling method and the molecular tools employed to resolve and quantify AMF taxa need to be improved and standardized to eliminate bias towards certain AMF strains and reduce discrepancies among studies. Lastly, inoculant producers must focus on selecting strains with a higher chance of success in the field, and having little or negligible downstream impacts.
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7
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Sweeney CJ, Bottoms M, Ellis S, Ernst G, Kimmel S, Loutseti S, Schimera A, Carniel LSC, Sharples A, Staab F, Marx MT. Arbuscular Mycorrhizal Fungi and the Need for a Meaningful Regulatory Plant Protection Product Testing Strategy. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:1808-1823. [PMID: 35678214 PMCID: PMC9543394 DOI: 10.1002/etc.5400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/23/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) perform key soil ecosystem services and, because of their symbiotic relationship with plant roots, may be exposed to the plant protection products (PPPs) applied to soils and crops. In 2017, the European Food Safety Authority (EFSA) released a scientific opinion addressing the state of the science on risk assessment of PPPs for in-soil organisms, recommending the inclusion of AMF ecotoxicological testing in the PPP regulatory process. However, it is not clear how this can be implemented in a tiered, robust, and ecologically relevant manner. Through a critical review of current literature, we examine the recommendations made within the EFSA report and the methodologies available to integrate AMF into the PPP risk assessment and provide perspective and commentary on their agronomic and ecological relevance. We conclude that considerable research questions remain to be addressed prior to the inclusion of AMF into the in-soil organism risk assessment, many of which stem from the unique challenges associated with including an obligate symbiont within the PPP risk assessment. Finally, we highlight critical knowledge gaps and the further research required to enable development of relevant, reliable, and robust scientific tests alongside pragmatic and scientifically sound guidance to ensure that any future risk-assessment paradigm is adequately protective of the ecosystem services it aims to preserve. Environ Toxicol Chem 2022;41:1808-1823. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
| | - Melanie Bottoms
- Syngenta, Jealott's Hill International Research Centre BracknellBracknellBerkshireUK
| | - Sian Ellis
- Corteva AgriscienceAbingdonOxfordshireUK
| | | | | | - Stefania Loutseti
- Syngenta, Jealott's Hill International Research Centre BracknellBracknellBerkshireUK
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Theelen B, Christinaki AC, Dawson TL, Boekhout T, Kouvelis VN. Comparative analysis of Malassezia furfur mitogenomes and the development of a mitochondria-based typing approach. FEMS Yeast Res 2021; 21:6375414. [PMID: 34562093 PMCID: PMC8510979 DOI: 10.1093/femsyr/foab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
Malassezia furfur is a yeast species belonging to Malasseziomycetes, Ustilaginomycotina and Basidiomycota that is found on healthy warm-blooded animal skin, but also involved in various skin disorders like seborrheic dermatitis/dandruff and pityriasis versicolor. Moreover, Malassezia are associated with bloodstream infections, Crohn's disease and pancreatic carcinoma. Recent advances in Malassezia genomics and genetics have focused on the nuclear genome. In this work, we present the M. furfur mitochondrial (mt) genetic heterogenicity with full analysis of 14 novel and six available M. furfur mt genomes. The mitogenome analysis reveals a mt gene content typical for fungi, including identification of variable mt regions suitable for intra-species discrimination. Three of them, namely the trnK–atp6 and cox3–nad3 intergenic regions and intron 2 of the cob gene, were selected for primer design to identify strain differences. Malassezia furfur strains belonging to known genetic variable clusters, based on AFLP and nuclear loci, were assessed for their mt variation using PCR amplification and sequencing. The results suggest that these mt regions are excellent molecular markers for the typing of M. furfur strains and may provide added value to nuclear regions when assessing evolutionary relationships at the intraspecies level.
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Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Anastasia C Christinaki
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Thomas L Dawson
- Agency for Science, Technology, and Research (A∗STAR), Skin Research Institute of Singapore (SRIS), 11 Mandalay Rd, #17-01, Singapore 308232, Singapore.,Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, 280 Calhoun St, Charleston, SC, 29425, USA
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
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9
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Megarioti AH, Kouvelis VN. The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG). Genome Biol Evol 2021; 12:1337-1354. [PMID: 32585032 PMCID: PMC7487136 DOI: 10.1093/gbe/evaa126] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Fungal mitochondrial (mt) genomes exhibit great diversity in size which is partially attributed to their variable intergenic regions and most importantly to the inclusion of introns within their genes. These introns belong to group I or II, and both of them are self-splicing. The majority of them carry genes encoding homing endonucleases, either LAGLIDADG or GIY-YIG. In this study, it was found that these intronic homing endonucleases genes (HEGs) may originate from mt free-standing open reading frames which can be found nowadays in species belonging to Early Diverging Fungi as “living fossils.” A total of 487 introns carrying HEGs which were located in the publicly available mt genomes of representative species belonging to orders from all fungal phyla was analyzed. Their distribution in the mt genes, their insertion target sequence, and the phylogenetic analyses of the HEGs showed that these introns along with their HEGs form a composite structure in which both selfish elements coevolved. The invasion of the ancestral free-standing HEGs in the introns occurred through a perpetual mechanism, called in this study as “aenaon” hypothesis. It is based on recombination, transpositions, and horizontal gene transfer events throughout evolution. HEGs phylogenetically clustered primarily according to their intron hosts and secondarily to the mt genes carrying the introns and their HEGs. The evolutionary models created revealed an “intron-early” evolution which was enriched by “intron-late” events through many different independent recombinational events which resulted from both vertical and horizontal gene transfers.
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Affiliation(s)
- Amalia H Megarioti
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
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10
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Wang B, Liang X, Hao X, Dang H, Hsiang T, Gleason ML, Zhang R, Sun G. Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in Botryosphaeria dothidea and B. kuwatsukai. Environ Microbiol 2021; 23:5320-5333. [PMID: 34029452 DOI: 10.1111/1462-2920.15608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 01/26/2023]
Abstract
Botryosphaeria dothidea is one of the most common fungal pathogens on a large number of hosts worldwide. Botryosphaeria dothidea and B. kuwatsukai are also the main causal agents of apple ring rot. In this study, we sequenced, assembled and annotated the circular mitogenomes of 12 diverse B. dothidea isolates (105.7-114.8 kb) infecting various plants including apple, and five diverse B. kuwatsukai isolates (118.0-124.6 kb) from apple. B. dothidea mitogenomes harboured a set of 29-31 introns and 48-52 ORFs. In contrast, B. kuwatsukai mitogenomes harboured more introns (32-34) and ORFs (51-54). The variation in mitogenome sizes was associated mainly with different numbers of introns and insertions of mobile genetic elements. Interestingly, B. dothidea and B. kuwatsukai displayed distinct intron distribution patterns, with three intron loci showing presence/absence dynamics in each species. Large numbers of introns (57% in B. dothidea and 49% in B. kuwatsukai) were most likely obtained through horizontal transfer from non-Dothideomycetes. The mitochondrial gene phylogeny supported the differentiation of the two species. Overall, this study sheds light into the mitochondrial evolution of the plant pathogens B. dothidea and B. kuwatsukai, and intron distribution patterns could be useful markers for studies on population diversity.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojuan Hao
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haiyue Dang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Thomsen C, Loverock L, Kokkoris V, Holland T, Bowen PA, Hart M. Commercial arbuscular mycorrhizal fungal inoculant failed to establish in a vineyard despite priority advantage. PeerJ 2021; 9:e11119. [PMID: 33981489 PMCID: PMC8071076 DOI: 10.7717/peerj.11119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
Background Arbuscular mycorrhizal (AM) fungi associate with most plants and can increase nutrient uptake. As a result, commercial inoculants called “biofertilizers” containing AM fungi have been developed and marketed to increase plant performance. However, successful establishment of these inoculants remains a challenge, and may be negatively impacted by competition with fungi already present (priority effects). Perennial agriculture may be more amenable if inoculants can be successfully established on crops prior to field planting. Methods Here, we inoculate grapevine (Vitis vinifera) with a commercial inoculant in three treatments designed to manipulate the strength and direction of priority effects and quantified the abundance of the fungal strain before and after introduction using droplet digital PCR (ddPCR). Results We found that the introduced strain did not establish in any treatment, even with priority advantage, and inoculated vines did not differ in performance from non-inoculated vines. Fungal abundance was not greater than in pre-inoculation soil samples during any of the five years sampled and may have been impaired by high available phosphorus levels in the soil. This study highlights the need to understand and evaluate how the management of the agricultural system will affect establishment before introduction of “biofertilizers”, which is often unpredictable.
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Affiliation(s)
- Corrina Thomsen
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Laura Loverock
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Taylor Holland
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Patricia A Bowen
- Summerland Research and Development Centre, Agriculture and Agri-food Canada, Summerland, BC, Canada
| | - Miranda Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada
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12
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Moustakas M, Bayçu G, Sperdouli I, Eroğlu H, Eleftheriou EP. Arbuscular Mycorrhizal Symbiosis Enhances Photosynthesis in the Medicinal Herb Salvia fruticosa by Improving Photosystem II Photochemistry. PLANTS 2020; 9:plants9080962. [PMID: 32751534 PMCID: PMC7463761 DOI: 10.3390/plants9080962] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/12/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023]
Abstract
We investigated the influence of Salvia fruticosa colonization by the arbuscular mycorrhizal fungi (AMF) Rhizophagus irregularis on photosynthetic function by using chlorophyll fluorescence imaging analysis to evaluate the light energy use in photosystem II (PSII) of inoculated and non-inoculated plants. We observed that inoculated plants used significantly higher absorbed energy in photochemistry (ΦPSII) than non-inoculated and exhibited significant lower excess excitation energy (EXC). However, the increased ΦPSII in inoculated plants did not result in a reduced non-regulated energy loss in PSII (ΦNO), suggesting the same singlet oxygen (1O2) formation between inoculated and non-inoculated plants. The increased ΦPSII in inoculated plants was due to an increased efficiency of open PSII centers to utilize the absorbed light (Fv'/Fm') due to a decreased non-photochemical quenching (NPQ) since there was no difference in the fraction of open reaction centers (qp). The decreased NPQ in inoculated plants resulted in an increased electron-transport rate (ETR) compared to non-inoculated. Yet, inoculated plants exhibited a higher efficiency of the water-splitting complex on the donor side of PSII as revealed by the increased Fv/Fo ratio. A spatial heterogeneity between the leaf tip and the leaf base for the parameters ΦPSII and ΦNPQ was observed in both inoculated and non-inoculated plants, reflecting different developmental zones. Overall, our findings suggest that the increased ETR of inoculated S. fruticosa contributes to increased photosynthetic performance, providing growth advantages to inoculated plants by increasing their aboveground biomass, mainly by increasing leaf biomass.
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Affiliation(s)
- Michael Moustakas
- Department of Biology, Faculty of Science, Istanbul University, 34134 Istanbul, Turkey; (G.B.); (H.E.)
- Department of Botany, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Correspondence: (M.M.); (E.P.E.)
| | - Gülriz Bayçu
- Department of Biology, Faculty of Science, Istanbul University, 34134 Istanbul, Turkey; (G.B.); (H.E.)
| | - Ilektra Sperdouli
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization-Demeter, Thermi, 57001 Thessaloniki, Greece;
| | - Hilal Eroğlu
- Department of Biology, Faculty of Science, Istanbul University, 34134 Istanbul, Turkey; (G.B.); (H.E.)
- Biology Division, Institute of Graduate Studies in Science, Istanbul University, 34134 Istanbul, Turkey
| | - Eleftherios P. Eleftheriou
- Department of Botany, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Correspondence: (M.M.); (E.P.E.)
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13
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina.,Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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14
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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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15
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Abstract
Biomass of arbuscular mycorrhizal fungi (AMF, Glomeromycota) is often only available in small quantities as these fungi are obligate biotrophs and many species are difficult to cultivate under controlled conditions. Here, I describe a simple, efficient approach to produce crude extracts from single or a small number of spores that can be used for genotyping AMF.
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16
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Li Q, Yang L, Xiang D, Wan Y, Wu Q, Huang W, Zhao G. The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): features, intron dynamics and phylogenetic implications. Int J Biol Macromol 2019; 145:974-984. [PMID: 31669472 DOI: 10.1016/j.ijbiomac.2019.09.188] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/10/2019] [Accepted: 09/20/2019] [Indexed: 10/25/2022]
Abstract
Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China; Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Luxi Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China.
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
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17
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Evolutionary history and genetic diversity study of heat-shock protein 60 of Rhizophagus irregularis. J Genet 2019. [DOI: 10.1007/s12041-019-1096-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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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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19
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Wang L, Zhang S, Li JH, Zhang YJ. Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungusHirsutella thompsonii. Environ Microbiol 2018; 20:3393-3405. [DOI: 10.1111/1462-2920.14379] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Lin Wang
- School of Life Science; Shanxi University; Taiyuan 030006 China
- Institute of Biotechnology; Shanxi University; Taiyuan 030006 China
| | - Shu Zhang
- Institute of Applied Chemistry; Shanxi University; Taiyuan 030006 China
| | - Jian-Hui Li
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu 030801 China
| | - Yong-Jie Zhang
- School of Life Science; Shanxi University; Taiyuan 030006 China
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20
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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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21
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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: 48] [Impact Index Per Article: 8.0] [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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Zhang YJ, Yang XQ, Zhang S, Humber RA, Xu J. Genomic analyses reveal low mitochondrial and high nuclear diversity in the cyclosporin-producing fungus Tolypocladium inflatum. Appl Microbiol Biotechnol 2017; 101:8517-8531. [PMID: 29034434 DOI: 10.1007/s00253-017-8574-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 12/18/2022]
Abstract
Mitochondrial DNA is generally regarded to evolve faster than nuclear DNA in animals, whereas if this is also true in fungi remains unclear. Herein, we annotate the first complete mitochondrial genome (mitogenome) of the cyclosporin-producing fungus Tolypocladium inflatum and report the genome-wide sequence variations among five isolates originating from distantly separated localities. We found that T. inflatum has among the most compact of fungal mitogenomes; its 25 kb DNA molecule encodes all standard fungal mitochondrial genes and harbors only one intron. Transcriptional analyses validated the expression of most conserved genes. We found several uncommon repetitive elements and evidence of gene transfer from the mitochondrion to the nucleus. Phylogenetic analyses confirmed the placement of T. inflatum in the fungal order Hypocreales although there was uncertainty on its family-level affiliation. Comparative genomic analyses among the five isolates identified an overall lower level of intraspecific variation in mitogenomes than in nuclear genomes; however, both the nuclear and mitochondrial genomes revealed similar isolate relationships, not correlating with geographic sources of these isolates. Our study shed new insights into the evolution of the medicinally important ascomycete T. inflatum.
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Affiliation(s)
- Yong-Jie Zhang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Xiao-Qing Yang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, China
| | - Richard A Humber
- USDA, ARS Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853-2901, USA
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.
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Franco MEE, López SMY, Medina R, Lucentini CG, Troncozo MI, Pastorino GN, Saparrat MCN, Balatti PA. The mitochondrial genome of the plant-pathogenic fungus Stemphylium lycopersici uncovers a dynamic structure due to repetitive and mobile elements. PLoS One 2017; 12:e0185545. [PMID: 28972995 PMCID: PMC5626475 DOI: 10.1371/journal.pone.0185545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/14/2017] [Indexed: 12/23/2022] Open
Abstract
Stemphylium lycopersici (Pleosporales) is a plant-pathogenic fungus that has been associated with a broad range of plant-hosts worldwide. It is one of the causative agents of gray leaf spot disease in tomato and pepper. The aim of this work was to characterize the mitochondrial genome of S. lycopersici CIDEFI-216, to use it to trace taxonomic relationships with other fungal taxa and to get insights into the evolutionary history of this phytopathogen. The complete mitochondrial genome was assembled into a circular double-stranded DNA molecule of 75,911 bp that harbors a set of 37 protein-coding genes, 2 rRNA genes (rns and rnl) and 28 tRNA genes, which are transcribed from both sense and antisense strands. Remarkably, its gene repertoire lacks both atp8 and atp9, contains a free-standing gene for the ribosomal protein S3 (rps3) and includes 13 genes with homing endonuclease domains that are mostly located within its 15 group I introns. Strikingly, subunits 1 and 2 of cytochrome oxidase are encoded by a single continuous open reading frame (ORF). A comparative mitogenomic analysis revealed the large extent of structural rearrangements among representatives of Pleosporales, showing the plasticity of their mitochondrial genomes. Finally, an exhaustive phylogenetic analysis of the subphylum Pezizomycotina based on mitochondrial data reconstructed their relationships in concordance with several studies based on nuclear data. This is the first report of a mitochondrial genome belonging to a representative of the family Pleosporaceae.
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Affiliation(s)
- Mario Emilio Ernesto Franco
- Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata - Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Buenos Aires, Argentina
| | - Silvina Marianela Yanil López
- Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata - Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Buenos Aires, Argentina
| | - Rocio Medina
- Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata - Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Buenos Aires, Argentina
| | - César Gustavo Lucentini
- Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata - Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Buenos Aires, Argentina
| | - Maria Inés Troncozo
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Graciela Noemí Pastorino
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Instituto de Botánica Carlos Spegazzini, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Instituto de Fisiología Vegetal, Facultad de Ciencias Naturales y Museo-Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata - Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata - Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail:
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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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Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris. Sci Rep 2017; 7:40219. [PMID: 28071691 PMCID: PMC5223169 DOI: 10.1038/srep40219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/02/2016] [Indexed: 12/18/2022] Open
Abstract
Cordyceps militaris is a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eight C. militaris strains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined.
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Mitochondrial DNA Based Molecular Markers in Arbuscular Mycorrhizal Fungi (AMF) Research. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Loján P, Senés-Guerrero C, Suárez JP, Kromann P, Schüßler A, Declerck S. Potato field-inoculation in Ecuador with Rhizophagus irregularis: no impact on growth performance and associated arbuscular mycorrhizal fungal communities. Symbiosis 2016. [DOI: 10.1007/s13199-016-0471-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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28
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Badri A, Stefani FOP, Lachance G, Roy-Arcand L, Beaudet D, Vialle A, Hijri M. Molecular diagnostic toolkit for Rhizophagus irregularis isolate DAOM-197198 using quantitative PCR assay targeting the mitochondrial genome. MYCORRHIZA 2016; 26:721-33. [PMID: 27220880 DOI: 10.1007/s00572-016-0708-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/09/2016] [Indexed: 05/09/2023]
Abstract
Rhizophagus irregularis (previously named Glomus irregulare) is one of the most widespread and common arbuscular mycorrhizal fungal (AMF) species. It has been recovered worldwide in agricultural and natural soils, and the isolate DAOM-197198 has been utilized as a commercial inoculant for two decades. Despite the ecological and economical importance of this taxon, specific markers for quantification of propagules by quantitative real-time PCR (qPCR) are extremely limited and none have been rigorously validated for quality control of manufactured products such as biofertilizers. From the sequencing of 14 complete AMF mitochondrial (mt) genomes, a qPCR assay using a hydrolysis probe designed in the single copy cox3-rnl intergenic region was tested and validated to specifically and accurately quantify the spores of R. irregularis isolate DAOM-197198. Specificity tests were performed using standard PCR and qPCR, and results clearly showed that the primers specifically amplified the isolate DAOM-197198, yielding a PCR product of 106 bp. According to the qPCR analyses on spores produced in vitro, the average copy number of mt genomes per spore was 3172 ± 304 SE (n = 6). Quantification assays were successfully undertaken on known and unknown samples in liquid suspensions and commercial dry formulations to show the accuracy, precision, robustness, and reproducibility of the qPCR assay. This study provides a powerful molecular toolkit specifically designed to quantify spores of the model AMF isolate DAOM-197198. The approach of molecular toolkit used in our study could be applied to other AMF taxa and will be useful to research institutions and governmental and industrial laboratories running routine quality control of AMF-based products.
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Affiliation(s)
- Amine Badri
- Centre de recherche sur les biotechnologies marines, 2e Rue Est, Rimouski, QC, G5L 9H3, Canada
| | - Franck O P Stefani
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Geneviève Lachance
- Premier Tech, 1 avenue Premier, Campus Premier Tech, Rivière-du-Loup, QC, G5R 6C1, Canada
| | - Line Roy-Arcand
- Premier Tech, 1 avenue Premier, Campus Premier Tech, Rivière-du-Loup, QC, G5R 6C1, Canada
| | - Denis Beaudet
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Agathe Vialle
- Biopterre-Centre de développement des bioproduits, 1642, Rue de la Ferme, La Pocatière, Québec, G0R 1Z0, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada.
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Nadimi M, Stefani FOP, Hijri M. The large (134.9 kb) mitochondrial genome of the glomeromycete Funneliformis mosseae. MYCORRHIZA 2016; 26:747-755. [PMID: 27246226 DOI: 10.1007/s00572-016-0710-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
Funneliformis mosseae is among the most ecologically and economically important glomeromycete species and occurs both in natural and disturbed areas in a wide range of habitats and climates. In this study, we report the sequencing of the complete mitochondrial (mt) genome of F. mosseae isolate FL299 using 454 pyrosequencing and Illumina HiSeq technologies. This mt genome is a full-length circular chromosome of 134,925 bp, placing it among the largest mitochondrial DNAs (mtDNAs) in the fungal kingdom. A comparative analysis with publically available arbuscular mycorrhizal fungal mtDNAs revealed that the mtDNA of F. mosseae FL299 contained a very large number of insertions contributing to its expansion. The gene synteny was completely reshuffled compared to previously published glomeromycotan mtDNAs and several genes were oriented in an anti-sense direction. Furthermore, the presence of different types of introns and insertions in rnl (14 introns) made this gene very distinctive in Glomeromycota. The presence of alternative genetic codes in both initiation (GUG) and termination (UGA) codons was another new feature in this mtDNA compared to previously published glomeromycotan mt genomes. The phylogenetic analysis inferred from the analysis of 14 protein mt genes confirmed the position of the Glomeromycota clade as a sister group of Mortierellomycotina. This mt genome is the largest observed so far in Glomeromycota and the first mt genome within the Funneliformis clade, providing new opportunities to better understand their evolution and to develop molecular markers.
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Affiliation(s)
- Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Franck O P Stefani
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC, H1X 2B2, Canada.
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Nadimi M, Daubois L, Hijri M. Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi. Mol Phylogenet Evol 2016; 98:74-83. [DOI: 10.1016/j.ympev.2016.01.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 12/16/2015] [Accepted: 01/14/2016] [Indexed: 11/29/2022]
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31
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Daubois L, Beaudet D, Hijri M, de la Providencia I. Independent mitochondrial and nuclear exchanges arising in Rhizophagus irregularis crossed-isolates support the presence of a mitochondrial segregation mechanism. BMC Microbiol 2016; 16:11. [PMID: 26803293 PMCID: PMC4724407 DOI: 10.1186/s12866-016-0627-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Arbuscular mycorrhizal fungi (AMF) are members of the phylum Glomeromycota, an early divergent fungal lineage that forms symbiotic associations with the large majority of land plants. These organisms are asexual obligate biotrophs, meaning that they cannot complete their life cycle in the absence of a suitable host. These fungi can exchange genetic information through hyphal fusions (i.e. anastomosis) with genetically compatible isolates belonging to the same species. The occurrence of transient mitochondrial length-heteroplasmy through anastomosis between geographically distant Rhizophagus irregularis isolates was previously demonstrated in single spores resulting from crossing experiments. However, (1) the persistence of this phenomenon in monosporal culture lines from crossed parental isolates, (2) its correlation with nuclear exchanges and (3) the potential mechanisms responsible for mitochondrial inheritance are still unknown. Using the AMF model organism R. irregularis, we tested whether the presence of a heteroplasmic state in progeny spores was linked to the occurrence of nuclear exchanges and whether the previously observed heteroplasmic state persisted in monosporal in vitro crossed-culture lines. We also investigated the presence of a putative mitochondrial segregation apparatus in Glomeromycota by identifying proteins similar to those found in other fungal groups. RESULTS We observed the occurrence of biparental inheritance both for mitochondrial and nuclear markers tested in single spores obtained from crossed-isolates. However, only one parental mitochondrial DNA and nuclear genotype were recovered in each monosporal crossed-cultures, with an overrepresentation of certain mitochondrial haplotypes. These results strongly support the presence of a nuclear-independent mitochondrial segregation mechanism in R. irregularis. Furthermore, a nearly complete set of genes was identified with putative orthology to those found in other fungi and known to be associated with the mitochondrial segregation in Saccharomyces cerevisiae and filamentous fungi. CONCLUSIONS Our findings suggest that mitochondrial segregation might take place either during spore formation or colony development and that it might be independent of the nuclear segregation machinery. We present the basic building blocks for a better understanding of the mitochondrial inheritance process and segregation in these important symbiotic fungi. The comprehension of these processes is of great importance since it has been shown that different segregated lines of the same isolate can have variable effects on the host plant.
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Affiliation(s)
- Laurence Daubois
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, QC, Canada.
| | - Denis Beaudet
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, QC, Canada.
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, QC, Canada.
| | - Ivan de la Providencia
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, QC, Canada.
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32
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Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Front Microbiol 2015; 6:996. [PMID: 26441923 PMCID: PMC4585241 DOI: 10.3389/fmicb.2015.00996] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/07/2015] [Indexed: 01/15/2023] Open
Abstract
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range.
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Affiliation(s)
- Susanna Atwell
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Jason A. Corwin
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Nicole E. Soltis
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Anushryia Subedy
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Katherine J. Denby
- School of Life Sciences and Warwick Systems Biology Centre, University of WarwickCoventry, UK
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Young JPW. Genome diversity in arbuscular mycorrhizal fungi. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:113-119. [PMID: 26190590 DOI: 10.1016/j.pbi.2015.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/28/2015] [Accepted: 06/06/2015] [Indexed: 06/04/2023]
Abstract
Arbuscular mycorrhizal fungi (Glomeromycota) are the most widespread and important symbionts of plants. They cannot be cultured without plants, are apparently asexual, and have multiple nuclei in a common cytoplasm. There is evidence for genetic variation among nuclei, and for segregation of this variation during growth, but these findings remain contentious. Recently, two papers have reported whole genome sequences for a strain of Rhizophagus irregularis; both suggest that genetic variation among nuclei is low. Genome assembly is very incomplete, though, so significant nuclear diversity cannot be excluded. While the diversity of nuclear genomes remains unresolved, multiple complete mitochondrial genomes are now available; there is virtually no variation within isolates, but significant variation between them.
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Affiliation(s)
- J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris. Fungal Genet Biol 2015; 77:95-107. [PMID: 25896956 DOI: 10.1016/j.fgb.2015.04.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/09/2015] [Accepted: 04/11/2015] [Indexed: 12/16/2022]
Abstract
Intra-specific comparison of mitochondrial genomes can help elucidate the evolution of a species, however it has not been performed for hypocrealean fungi that form diverse symbiotic associations with other organisms. In this study, comparative analyses of three completely sequenced mitochondrial genomes of a hypocrealean fungus, Cordyceps militaris, the type species of Cordyceps genus, revealed that the introns were the main contributors to mitochondrial genome size variations among strains. Mitochondrial genes in C. militaris have been invaded by group I introns in at least eight positions. PCR assays of various C. militaris isolates showed abundant variations of intron presence/absence among strains at seven of the eight intronic loci. Although the ancestral intron pattern was inferred to contain all eight introns, loss and/or gain events occurred for seven of the eight introns. These introns invaded the C. militaris mitochondrial genome probably by horizontal transfer from other fungi, and intron insertions into intronless genes in C. militaris were accompanied by co-conversions of upstream exon sequences especially for those introns targeting protein-coding genes. We also detected phylogenetic congruence between the intron and exon trees at each individual locus, consistent with the ancestral mitochondria of C. militaris as having all eight introns. This study helps to explain the evolution of C. militaris mitochondrial genomes and will facilitate population genetic studies of this medicinally important fungus.
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Nadimi M, Stefani FOP, Hijri M. The mitochondrial genome of the glomeromycete Rhizophagus sp. DAOM 213198 reveals an unusual organization consisting of two circular chromosomes. Genome Biol Evol 2014; 7:96-105. [PMID: 25527840 PMCID: PMC4316621 DOI: 10.1093/gbe/evu268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2014] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial (mt) genomes are intensively studied in Ascomycota and Basidiomycota, but they are poorly documented in basal fungal lineages. In this study, we sequenced the complete mtDNA of Rhizophagus sp. DAOM 213198, a close relative to Rhizophagus irregularis, a widespread, ecologically and economical relevant species belonging to Glomeromycota. Unlike all other known taxonomically close relatives harboring a full-length circular chromosome, mtDNA of Rhizophagus sp. reveals an unusual organization with two circular chromosomes of 61,964 and 29,078 bp. The large chromosome contained nine protein-coding genes (atp9, nad5, cob, nad4, nad1, nad4L, cox1, cox2, and atp8), small subunit rRNA gene (rns), and harbored 20 tRNA-coding genes and 10 orfs, while the small chromosome contained five protein-coding genes (atp6, nad2, nad3, nad6, and cox3), large subunit rRNA gene (rnl) in addition to 5 tRNA-coding genes, and 8 plasmid-related DNA polymerases (dpo). Although structural variation of plant mt genomes is well documented, this study is the first report of the presence of two circular mt genomes in arbuscular mycorrhizal fungi. Interestingly, the presence of dpo at the breakage point in intergenes cox1-cox2 and rnl-atp6 for large and small mtDNAs, respectively, could be responsible for the conversion of Rhizophagus sp. mtDNA into two chromosomes. Using quantitative real-time polymerase chain reaction, we found that both mtDNAs have an equal abundance. This study reports a novel mtDNA organization in Glomeromycota and highlights the importance of studying early divergent fungal lineages to describe novel evolutionary pathways in the fungal kingdom.
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Affiliation(s)
- Maryam Nadimi
- Département de Sciences Biologiques, Université de Montréal, Institut de Recherche en Biologie Végétale (IRBV), Quebec, Canada
| | - Franck O P Stefani
- Département de Sciences Biologiques, Université de Montréal, Institut de Recherche en Biologie Végétale (IRBV), Quebec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Université de Montréal, Institut de Recherche en Biologie Végétale (IRBV), Quebec, Canada
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Beaudet D, de la Providencia IE, Labridy M, Roy-Bolduc A, Daubois L, Hijri M. Intraisolate mitochondrial genetic polymorphism and gene variants coexpression in arbuscular mycorrhizal fungi. Genome Biol Evol 2014; 7:218-27. [PMID: 25527836 PMCID: PMC4316628 DOI: 10.1093/gbe/evu275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2014] [Indexed: 11/13/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are multinucleated and coenocytic organisms, in which the extent of the intraisolate nuclear genetic variation has been a source of debate. Conversely, their mitochondrial genomes (mtDNAs) have appeared to be homogeneous within isolates in all next generation sequencing (NGS)-based studies. Although several lines of evidence have challenged mtDNA homogeneity in AMF, extensive survey to investigate intraisolate allelic diversity has not previously been undertaken. In this study, we used a conventional polymerase chain reaction -based approach on selected mitochondrial regions with a high-fidelity DNA polymerase, followed by cloning and Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivated in vitro for several generations (DAOM-197198) and the other recently isolated from the field (DAOM-242422). At different loci in both isolates, we found intraisolate allelic variation within the mtDNA and in a single copy nuclear marker, which highlighted the presence of several nonsynonymous mutations in protein coding genes. We confirmed that some of this variation persisted in the transcriptome, giving rise to at least four distinct nad4 transcripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary process in AMF. Our study reveals that genetic variation in Glomeromycota is higher than what had been previously assumed and also suggests that it could have been grossly underestimated in most NGS-based AMF studies, both in mitochondrial and nuclear genomes, due to the presence of low-level mutations.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Ivan Enrique de la Providencia
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Manuel Labridy
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Alice Roy-Bolduc
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Laurence Daubois
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
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Hafez M, Guha TK, Hausner G. I-OmiI and I-OmiII: two intron-encoded homing endonucleases within the Ophiostoma minus rns gene. Fungal Biol 2014; 118:721-31. [PMID: 25110134 DOI: 10.1016/j.funbio.2014.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/08/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022]
Abstract
The mitochondrial small subunit ribosomal RNA (rns) gene of the ascomycetous fungus Ophiostoma minus [strain WIN(M)371] was found to contain a group IC2 and a group IIB1 intron at positions mS569 and mS952 respectively. Both introns have open reading frames (ORFs) embedded that encode double motif LAGLIDADG homing endonucleases (I-OmiI and I-OmiII respectively). Codon-optimized versions of I-OmiI and I-OmiII were synthesized for overexpression in Escherichia coli. The in vitro characterization of I-OmiII showed that it is a functional homing endonuclease that cleaves the rns target site two nucleotides upstream (sense strand) of the intron insertion site generating 4 nucleotide 3' overhangs. The endonuclease activity of I-OmiII was tested using linear and circular substrates and cleavage activity was evaluated at various temperatures. The I-OmiI protein was expressed in E. coli, but purification was difficult, thus the endonuclease activity of this protein was tested via in vivo assays. Overall this study showed that there are many native forms of functional homing endonucleases yet to be discovered among fungal mtDNA genomes.
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Affiliation(s)
- Mohamed Hafez
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Botany, Faculty of Science, Suez University, Suez, Egypt
| | - Tuhin Kumar Guha
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Borriello R, Bianciotto V, Orgiazzi A, Lumini E, Bergero R. Sequencing and comparison of the mitochondrial COI gene from isolates of Arbuscular Mycorrhizal Fungi belonging to Gigasporaceae and Glomeraceae families. Mol Phylogenet Evol 2014; 75:1-10. [PMID: 24569015 DOI: 10.1016/j.ympev.2014.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/16/2022]
Abstract
Arbuscular Mycorrhizal Fungi (AMF) are well known for their ecological importance and their positive influence on plants. The genetics and phylogeny of this group of fungi have long been debated. Nuclear markers are the main tools used for phylogenetic analyses, but they have sometimes proved difficult to use because of their extreme variability. Therefore, the attention of researchers has been moving towards other genomic markers, in particular those from the mitochondrial DNA. In this study, 46 sequences of different AMF isolates belonging to two main clades Gigasporaceae and Glomeraceae have been obtained from the mitochondrial gene coding for the Cytochrome c Oxidase I (COI), representing the largest dataset to date of AMF COI sequences. A very low level of divergence was recorded in the COI sequences from the Gigasporaceae, which could reflect either a slow rate of evolution or a more recent evolutionary divergence of this group. On the other hand, the COI sequence divergence between Gigasporaceae and Glomeraceae was high, with synonymous divergence reaching saturated levels. This work also showed the difficulty in developing valuable mitochondrial markers able to effectively distinguish all Glomeromycota species, especially those belonging to Gigasporaceae, yet it represents a first step towards the development of a full mtDNA-based dataset which can be used for further phylogenetic investigations of this fungal phylum.
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Affiliation(s)
- Roberto Borriello
- Plant Protection Institute (IPP)-Turin UOS, National Research Council (CNR), c/o Department of Life Science and Systems Biology, University of Turin, Viale P.A. Mattioli 25, Turin 10125, Italy
| | - Valeria Bianciotto
- Plant Protection Institute (IPP)-Turin UOS, National Research Council (CNR), c/o Department of Life Science and Systems Biology, University of Turin, Viale P.A. Mattioli 25, Turin 10125, Italy
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, Via E. Fermi, 2749, Ispra, VA I-21027, Italy
| | - Erica Lumini
- Plant Protection Institute (IPP)-Turin UOS, National Research Council (CNR), c/o Department of Life Science and Systems Biology, University of Turin, Viale P.A. Mattioli 25, Turin 10125, Italy.
| | - Roberta Bergero
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
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Evolutionary dynamics of introns and their open reading frames in the U7 region of the mitochondrial rnl gene in species of Ceratocystis. Fungal Biol 2013; 117:791-806. [DOI: 10.1016/j.funbio.2013.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/12/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022]
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de la Providencia IE, Nadimi M, Beaudet D, Rodriguez Morales G, Hijri M. Detection of a transient mitochondrial DNA heteroplasmy in the progeny of crossed genetically divergent isolates of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2013; 200:211-221. [PMID: 23790215 DOI: 10.1111/nph.12372] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Abstract
Nonself fusion and nuclear genetic exchange have been documented in arbuscular mycorrhizal fungi (AMF), particularly in Rhizophagus irregularis. However, mitochondrial transmission accompanying nonself fusion of genetically divergent isolates remains unknown. Here, we tested the hypothesis that mitochondrial DNA (mtDNA) heteroplasmy occurs in the progeny of spores, obtained by crossing genetically divergent mtDNAs in R. irregularis isolates. Three isolates of geographically distant locations were used to investigate nonself fusions and mtDNA transmission to the progeny. We sequenced two additional mtDNAs of two R. irregularis isolates and developed isolate-specific size-variable markers in intergenic regions of these isolates and those of DAOM-197198. We achieved three crossing combinations in pre-symbiotic and symbiotic phases. Progeny spores per crossing combination were genotyped using isolate-specific markers. We found evidence that nonself recognition occurs between isolates originating from different continents both in pre-symbiotic and symbiotic phases. Genotyping patterns of individual spores from the progeny clearly showed the presence of markers of the two parental mtDNA haplotypes. Our results demonstrate that mtDNA heteroplasmy occurs in the progeny of the crossed isolates. However, this heteroplasmy appears to be a transient stage because all the live progeny spores that were able to germinate showed only one mtDNA haplotype.
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Affiliation(s)
- Ivan Enrique de la Providencia
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Denis Beaudet
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Gabriela Rodriguez Morales
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
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Beaudet D, Nadimi M, Iffis B, Hijri M. Rapid mitochondrial genome evolution through invasion of mobile elements in two closely related species of arbuscular mycorrhizal fungi. PLoS One 2013; 8:e60768. [PMID: 23637766 PMCID: PMC3630166 DOI: 10.1371/journal.pone.0060768] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/02/2013] [Indexed: 11/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are common and important plant symbionts. They have coenocytic hyphae and form multinucleated spores. The nuclear genome of AMF is polymorphic and its organization is not well understood, which makes the development of reliable molecular markers challenging. In stark contrast, their mitochondrial genome (mtDNA) is homogeneous. To assess the intra- and inter-specific mitochondrial variability in closely related Glomus species, we performed 454 sequencing on total genomic DNA of Glomus sp. isolate DAOM-229456 and we compared its mtDNA with two G. irregulare isolates. We found that the mtDNA of Glomus sp. is homogeneous, identical in gene order and, with respect to the sequences of coding regions, almost identical to G. irregulare. However, certain genomic regions vary substantially, due to insertions/deletions of elements such as introns, mitochondrial plasmid-like DNA polymerase genes and mobile open reading frames. We found no evidence of mitochondrial or cytoplasmic plasmids in Glomus species, and mobile ORFs in Glomus are responsible for the formation of four gene hybrids in atp6, atp9, cox2, and nad3, which are most probably the result of horizontal gene transfer and are expressed at the mRNA level. We found evidence for substantial sequence variation in defined regions of mtDNA, even among closely related isolates with otherwise identical coding gene sequences. This variation makes it possible to design reliable intra- and inter-specific markers.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Maryam Nadimi
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Bachir Iffis
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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Beaudet D, Terrat Y, Halary S, de la Providencia IE, Hijri M. Mitochondrial genome rearrangements in glomus species triggered by homologous recombination between distinct mtDNA haplotypes. Genome Biol Evol 2013; 5:1628-43. [PMID: 23925788 PMCID: PMC3787672 DOI: 10.1093/gbe/evt120] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2013] [Indexed: 02/02/2023] Open
Abstract
Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms.AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes (dpo), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp.) with substantial mtDNA synteny divergence,were sequenced and compared with available glomeromycotan mitochondrial genomes. We used an extensive nucleotide/protein similarity network-based approach to investigated podiversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo-induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity.We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | | | | | - Ivan Enrique de la Providencia
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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Corradi N, Bonen L. Mitochondrial genome invaders: an unselfish role as molecular markers. THE NEW PHYTOLOGIST 2012; 196:963-965. [PMID: 23121186 DOI: 10.1111/j.1469-8137.2012.04354.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Linda Bonen
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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