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Lofgren L, Nguyen NH, Kennedy P, Pérez-Pazos E, Fletcher J, Liao HL, Wang H, Zhang K, Ruytinx J, Smith AH, Ke YH, Cotter HVT, Engwall E, Hameed KM, Vilgalys R, Branco S. Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution. THE NEW PHYTOLOGIST 2024; 242:1448-1475. [PMID: 38581203 PMCID: PMC11045321 DOI: 10.1111/nph.19700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.
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Affiliation(s)
- Lotus Lofgren
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Māno, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Eduardo Pérez-Pazos
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1475 Gortner Ave, Saint Paul, MN 55108, USA
| | - Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Haihua Wang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
- Department of Soil, Water and Ecosystem Sciences, University of Florida, 1692 McCarty Dr, Room 2181, Building A, Gainesville, FL 32611, USA
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Rd Quincy, FL 3235, USA
| | - Joske Ruytinx
- Research Group of Microbiology and Plant Genetics, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium, USA
| | - Alexander H. Smith
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
| | - Yi-Hong Ke
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 N University Ave, Ann Arbor, MI 48109, USA
| | - H. Van T. Cotter
- University of North Carolina at Chapel Hill Herbarium, 120 South Road, Chapel Hill, NC 27599, USA
| | - Eiona Engwall
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA
| | - Khalid M. Hameed
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, 130 Science Dr., Durham, NC 27708, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA
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2
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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3
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Plett KL, Wojtalewicz D, Anderson IC, Plett JM. Fungal metabolism and free amino acid content may predict nitrogen transfer to the host plant in the ectomycorrhizal relationship between Pisolithus spp. and Eucalyptus grandis. THE NEW PHYTOLOGIST 2024; 242:1589-1602. [PMID: 37974494 DOI: 10.1111/nph.19400] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition; however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition, resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus, known to have significant variability in colonisation and transfer of nutrients to a host. We considered the metabolic fate of N acquired by the fungi and found that the percentage of plant N acquired through symbiosis significantly correlated to the concentration of free amino acids in ECM extra-radical mycelium. Transcriptomic analyses complemented these findings with isolates having high amino acid content and N transfer showing increased expression of genes related to amino acid transport and catabolic pathways. These results suggest that fungal N metabolism impacts N transfer to the host plant in this interaction and that relative N transfer may be possible to predict through basic biochemical analyses.
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Affiliation(s)
- Krista L Plett
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, 2568, Australia
| | - Dominika Wojtalewicz
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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4
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Furtado ANM, de Farias ST, Maia MDS. Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor. Biosystems 2024; 238:105194. [PMID: 38513884 DOI: 10.1016/j.biosystems.2024.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/29/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
•The signaling process during mycorrhiza establishment involves intense molecular communication between symbionts. It has been suggested that a group of protein effectors, the so-called MiSSPs, plays a broader function in the symbiosis metabolism, however, many of these remain uncharacterized structurally and functionally. •Herein we used three-dimensional protein structure modeling methods, ligand analysis, and molecular docking to structurally characterize and describe two protein effectors, MiSSP13 and MiSSP16.5, with enhanced expression during the mycorrhizal process in Laccaria bicolor. •MiSSP13 and MiSSP16.5 show structural homology with the cysteine and aspartate protease inhibitor, cocaprin (CCP1). Through structural analysis, it was observed that MiSSP13 and MiSSP16.5 have an active site similar to that observed in CCP1. The protein-protein docking data showed that MiSSP13 and MiSSP16.5 interact with the papain and pepsin proteases at sites that are near to where CCP1 interacts with these same targets, suggesting a function as inhibitor of cysteine and aspartate proteases. The interaction of MiSSP13 with papain and MiSSP16.5 with pepsin was stronger than the interaction of CCP1 with these proteases, suggesting that the MiSSPs had a greater activity in inhibiting these classes of proteases. Based on the data supplied, a model is proposed for the function of MiSSPs 13 and 16.5 during the symbiosis establishment. Our findings, while derived from in silico analyses, enable us formulate intriguing hypothesis on the function of MiSSPs in ectomycorrhization, which will require experimental validation.
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Affiliation(s)
- Ariadne N M Furtado
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil.
| | - Sávio Torres de Farias
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil; Network of Researchers on Chemical Emergence of Life (NoRCEL), Leeds, LS7 3RB, UK
| | - Mayara Dos Santos Maia
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil
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Maillard F, Kohler A, Morin E, Hossann C, Miyauchi S, Ziegler-Devin I, Gérant D, Angeli N, Lipzen A, Keymanesh K, Johnson J, Barry K, Grigoriev IV, Martin FM, Buée M. Functional genomics gives new insights into the ectomycorrhizal degradation of chitin. THE NEW PHYTOLOGIST 2023; 238:845-858. [PMID: 36702619 DOI: 10.1111/nph.18773] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Ectomycorrhizal (EcM) fungi play a crucial role in the mineral nitrogen (N) nutrition of their host trees. While it has been proposed that several EcM species also mobilize organic N, studies reporting the EcM ability to degrade N-containing polymers, such as chitin, remain scarce. Here, we assessed the capacity of a representative collection of 16 EcM species to acquire 15 N from 15 N-chitin. In addition, we combined genomics and transcriptomics to identify pathways involved in exogenous chitin degradation between these fungal strains. Boletus edulis, Imleria badia, Suillus luteus, and Hebeloma cylindrosporum efficiently mobilized N from exogenous chitin. EcM genomes primarily contained genes encoding for the direct hydrolysis of chitin. Further, we found a significant relationship between the capacity of EcM fungi to assimilate organic N from chitin and their genomic and transcriptomic potentials for chitin degradation. These findings demonstrate that certain EcM fungal species depolymerize chitin using hydrolytic mechanisms and that endochitinases, but not exochitinases, represent the enzymatic bottleneck of chitin degradation. Finally, this study shows that the degradation of exogenous chitin by EcM fungi might be a key functional trait of nutrient cycling in forests dominated by EcM fungi.
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Affiliation(s)
- François Maillard
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Christian Hossann
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | | | - Dominique Gérant
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, 54000, Nancy, France
| | - Nicolas Angeli
- Université de Lorraine, AgroParisTech, INRAE, SILVA, Silvatech, F-54000, Nancy, France
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, 54280, Champenoux, France
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Tsers I, Marenina E, Meshcherov A, Petrova O, Gogoleva O, Tkachenko A, Gogoleva N, Gogolev Y, Potapenko E, Muraeva O, Ponomareva M, Korzun V, Gorshkov V. First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale. IMA Fungus 2023; 14:2. [PMID: 36627722 PMCID: PMC9830731 DOI: 10.1186/s43008-022-00107-0] [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: 08/20/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.
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Affiliation(s)
- Ivan Tsers
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Ekaterina Marenina
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Azat Meshcherov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Petrova
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Alexander Tkachenko
- grid.35915.3b0000 0001 0413 4629Laboratory of Computer Technologies, ITMO University, Saint Petersburg, Russia 197101
| | - Natalia Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Yuri Gogolev
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Evgenii Potapenko
- grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, 3498838 Haifa, Israel ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
| | - Olga Muraeva
- grid.512700.1Bioinformatics Institute, Saint Petersburg, Russia 197342
| | - Mira Ponomareva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Viktor Korzun
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111 ,grid.425691.dKWS SAAT SE & Co. KGaA, 37555 Einbeck, Germany
| | - Vladimir Gorshkov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
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7
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Feng W, Sun X, Ding G. Morphological and Transcriptional Characteristics of the Symbiotic Interaction between Pinus massoniana and Suillus bovinus. J Fungi (Basel) 2022; 8:1162. [PMID: 36354929 PMCID: PMC9699607 DOI: 10.3390/jof8111162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Ectomycorrhiza (ECM) function has been well studied; however, there is little detailed information regarding the establishment of ECM symbioses. We investigated the morphological and transcriptional changes that occur during the establishment of the Pinus massoniana-Suillus bovinus ECM. S. bovinus promoted the growth of P. massoniana via the release of volatile organic compounds and exudates during the pre-symbiotic stage. Exudate-induced effects showed host plant specificity. At seven days post-inoculation (dpi), the mycelium started to penetrate P. massoniana roots. At 28 dpi, the Hartig net and mantle formed. At the pre-symbiotic stage, most differentially expressed genes in P. massoniana roots were mapped to the biosynthesis of secondary metabolites, signal transduction, and carbohydrate metabolism. At the symbiotic stage, S. bovinus colonization induced the reprogramming of pathways involved in genetic information processing in P. massoniana, particularly at the Hartig net and mantle formation stage. Phenylpropanoid biosynthesis was present at all stages and was regulated via S. bovinus colonization. Enzyme inhibitor tests suggested that hydroxycinnamoyl-CoA shikimate/quinate transferase is involved in the development of the Hartig net. Our findings outline the mechanism involved in the P. massoniana-S. bovinus ECM. Further studies are needed to clarify the role of phenylpropanoid biosynthesis in ECM formation.
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Affiliation(s)
- Wanyan Feng
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang 550025, China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Xueguang Sun
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang 550025, China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Guijie Ding
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang 550025, China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Forestry, Guizhou University, Guiyang 550025, China
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8
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Sakamoto Y, Sato S, Takizawa M, Narimatsu M. Identification of up-regulated genes in Tricholoma matsutake mycorrhiza. FEMS Microbiol Lett 2022; 369:6678003. [PMID: 36029515 DOI: 10.1093/femsle/fnac085] [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: 09/30/2021] [Revised: 06/23/2022] [Accepted: 08/25/2022] [Indexed: 11/12/2022] Open
Abstract
Many plant roots associate with fungi to form mycorrhizae; tree roots especially associate with ectomycorrhizal fungi, such as Tricholoma species. Tricholoma matsutake is an economically important fungus in Asian countries and usually inhabits forests primarily composed of Pinus densiflora (Japanese red pine). In this study, to understand the mycorrhizal association between T. matsutake and P. densiflora, genes specifically expressed in mycorrhiza compared with those expressed in mycelia and fruiting bodies were identified by RNA-seq. This revealed that genes for chromatin, proteasomes, signal transduction, pheromones, cell surface receptors, cytoskeleton, RNA processing, and transporters from T. matsutake were highly expressed in mycorrhiza. It also identified 35 mycorrhiza-induced small secreted protein (MiSSPs) that were highly expressed in mycorrhiza. Meanwhile, genes for proteases, defence-related proteins, cell-wall degradation, signal transduction, pinene synthesis, plant hormones, and transporters from P. densiflora were highly expressed in mycorrhiza. These genes may be involved in mycorrhizal formation and maintenance. A MiSSP, 1 460 819, was highly expressed in mycorrhiza, and this expression was maintained for 24 months. These results provide insight into the mycorrhizal association between T. matsutake and P. densiflora.
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Affiliation(s)
- Yuichi Sakamoto
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Shiho Sato
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Miyuki Takizawa
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Maki Narimatsu
- Iwate Prefectural Forest Technology Center, 560-11 Kemuyama, Yahaba, Iwate 028-3623, Japan
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9
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Lebreton A, Tang N, Kuo A, LaButti K, Andreopoulos W, Drula E, Miyauchi S, Barry K, Clum A, Lipzen A, Mousain D, Ng V, Wang R, Dai Y, Henrissat B, Grigoriev IV, Guerin-Laguette A, Yu F, Martin FM. Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap (Lactarius) mushrooms. THE NEW PHYTOLOGIST 2022; 235:306-319. [PMID: 35383395 DOI: 10.1111/nph.18143] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
| | - Nianwu Tang
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Elodie Drula
- CNRS, Aix-Marseille Université, Marseille, 13288, France
- USC1408 AFMB, INRAE, Marseille, 13288, France
| | - Shingo Miyauchi
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | | | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Ran Wang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Alexis Guerin-Laguette
- Mycotree C/- Southern Woods Nursery, 1002 Robinsons Road, RD8, Christchurch, 7678, New Zealand
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Francis M Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, Unité mixte de recherche Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, 54280, Champenoux, France
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A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor. Microorganisms 2021; 9:microorganisms9122612. [PMID: 34946213 PMCID: PMC8708209 DOI: 10.3390/microorganisms9122612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 02/05/2023] Open
Abstract
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.
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