1
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Auer L, Buée M, Fauchery L, Lombard V, Barry KW, Clum A, Copeland A, Daum C, Foster B, LaButti K, Singan V, Yoshinaga Y, Martineau C, Alfaro M, Castillo FJ, Imbert JB, Ramírez L, Castanera R, Pisabarro AG, Finlay R, Lindahl B, Olson A, Séguin A, Kohler A, Henrissat B, Grigoriev IV, Martin FM. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. New Phytol 2024; 242:1676-1690. [PMID: 38148573 DOI: 10.1111/nph.19471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/23/2023] [Indexed: 12/28/2023]
Abstract
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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Affiliation(s)
- Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, Marseille, 13288, France
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, 13009, France
| | - Kerry W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Federico J Castillo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - J Bosco Imbert
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Lucia Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Roger Finlay
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Björn Lindahl
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Ake Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Bernard Henrissat
- DTU Bioengineering, Denmarks Tekniske Universitet, Copenhagen, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 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 Interactions Arbres-Microorganismes, Nancy, F-54000, France
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2
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Mathieu D, Bryson AE, Hamberger B, Singan V, Keymanesh K, Wang M, Barry K, Mondo S, Pangilinan J, Koriabine M, Grigoriev IV, Bonito G, Hamberger B. Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long-standing interaction among land plants and fungi. Plant J 2024; 118:304-323. [PMID: 38265362 DOI: 10.1111/tpj.16605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/16/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant-fungal interactions today, it is hypothesized these kingdoms have a long-standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free-living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia, interact with P. patens in coculture. We also assess how Mollicute-related or Burkholderia-related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high-throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant-fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens.
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Affiliation(s)
- Davis Mathieu
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Abigail E Bryson
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Britta Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Keykhosrow Keymanesh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, 94720, USA
| | - Gregory Bonito
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Björn Hamberger
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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3
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Marqués-Gálvez JE, Pandharikar G, Basso V, Kohler A, Lackus ND, Barry K, Keymanesh K, Johnson J, Singan V, Grigoriev IV, Vilgalys R, Martin F, Veneault-Fourrey C. Populus MYC2 orchestrates root transcriptional reprogramming of defence pathway to impair Laccaria bicolor ectomycorrhizal development. New Phytol 2024; 242:658-674. [PMID: 38375883 DOI: 10.1111/nph.19609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024]
Abstract
The jasmonic acid (JA) signalling pathway plays an important role in the establishment of the ectomycorrhizal symbiosis. The Laccaria bicolor effector MiSSP7 stabilizes JA corepressor JAZ6, thereby inhibiting the activity of Populus MYC2 transcription factors. Although the role of MYC2 in orchestrating plant defences against pathogens is well established, its exact contribution to ECM symbiosis remains unclear. This information is crucial for understanding the balance between plant immunity and symbiotic relationships. Transgenic poplars overexpressing or silencing for the two paralogues of MYC2 transcription factor (MYC2s) were produced, and their ability to establish ectomycorrhiza was assessed. Transcriptomics and DNA affinity purification sequencing were performed. MYC2s overexpression led to a decrease in fungal colonization, whereas its silencing increased it. The enrichment of terpene synthase genes in the MYC2-regulated gene set suggests a complex interplay between the host monoterpenes and fungal growth. Several root monoterpenes have been identified as inhibitors of fungal growth and ECM symbiosis. Our results highlight the significance of poplar MYC2s and terpenes in mutualistic symbiosis by controlling root fungal colonization. We identified poplar genes which direct or indirect control by MYC2 is required for ECM establishment. These findings deepen our understanding of the molecular mechanisms underlying ECM symbiosis.
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Affiliation(s)
- José Eduardo Marqués-Gálvez
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Gaurav Pandharikar
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Veronica Basso
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Nathalie D Lackus
- Lehrstuhl für Pharmazeutische Biologie, Julius-von-Sachs-Institut für Biowissenschaften, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs-Platz 2, Würzburg, 97082, Deutschland
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux, 54280, France
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4
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Lei L, Gordon SP, Liu L, Sade N, Lovell JT, Rubio Wilhelmi MDM, Singan V, Sreedasyam A, Hestrin R, Phillips J, Hernandez BT, Barry K, Shu S, Jenkins J, Schmutz J, Goodstein DM, Thilmony R, Blumwald E, Vogel JP. The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum. G3 (Bethesda) 2023; 14:jkad245. [PMID: 37883711 PMCID: PMC10755203 DOI: 10.1093/g3journal/jkad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.
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Affiliation(s)
- Li Lei
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sean P Gordon
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lifeng Liu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nir Sade
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - John T Lovell
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Rachel Hestrin
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jeremy Phillips
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bryan T Hernandez
- Crop Improvement and Genetics Research Unit, USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David M Goodstein
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Roger Thilmony
- Crop Improvement and Genetics Research Unit, USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - John P Vogel
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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5
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Amses K, Desiró A, Bryson A, Grigoriev I, Mondo S, Lipzen A, LaButti K, Riley R, Singan V, Salazar-Hamm P, King J, Ballou E, Pawlowska T, Adeleke R, Bonito G, Uehling J. Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi. Fungal Genet Biol 2023; 169:103838. [PMID: 37716699 DOI: 10.1016/j.fgb.2023.103838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.
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Affiliation(s)
- Kevin Amses
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Alessandro Desiró
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Abigail Bryson
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Igor Grigoriev
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stephen Mondo
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vasanth Singan
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paris Salazar-Hamm
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Jason King
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth Ballou
- School of Biosciences, University of Sheffield, Western Bank S10 2TN, UK
| | - Teresa Pawlowska
- MRC Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, UK
| | - Rasheed Adeleke
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904, USA; Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Private bag X6001, 2520, South Africa
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Jessie Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA.
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6
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McRae AG, Taneja J, Yee K, Shi X, Haridas S, LaButti K, Singan V, Grigoriev IV, Wildermuth MC. Spray-induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control. Mol Plant Pathol 2023; 24:1168-1183. [PMID: 37340595 PMCID: PMC10423327 DOI: 10.1111/mpp.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 06/22/2023]
Abstract
Spray-induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double-stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole-fungicide target cytochrome P450 51 (CYP51) in the Golovinomyces orontii-Arabidopsis thaliana pathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation: apoptosis-antagonizing transcription factor in essential cellular metabolism and stress response; lipid catabolism genes lipase a, lipase 1, and acetyl-CoA oxidase in energy production; and genes involved in manipulation of the plant host via abscisic acid metabolism (9-cis-epoxycarotenoid dioxygenase, xanthoxin dehydrogenase, and a putative abscisic acid G-protein coupled receptor) and secretion of the effector protein, effector candidate 2. Powdery mildew is the dominant disease impacting grapes and extensive powdery mildew resistance to applied fungicides has been reported. We therefore developed SIGS for the Erysiphe necator-Vitis vinifera system and tested six successful targets identified using the G. orontii-A. thaliana system. For all targets tested, a similar reduction in powdery mildew disease was observed between systems. This indicates screening of broadly conserved targets in the G. orontii-A. thaliana pathosystem identifies targets and processes for the successful control of other powdery mildew fungi. The efficacy of SIGS on powdery mildew fungi makes SIGS an exciting prospect for commercial powdery mildew control.
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Affiliation(s)
- Amanda G. McRae
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jyoti Taneja
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kathleen Yee
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Xinyi Shi
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Sajeet Haridas
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Kurt LaButti
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Vasanth Singan
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Igor V. Grigoriev
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Mary C. Wildermuth
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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7
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Brown JL, Gierke T, Butkovich LV, Swift CL, Singan V, Daum C, Barry K, Grigoriev IV, O’Malley MA. High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi. Front Fungal Biol 2023; 4:1171100. [PMID: 37746117 PMCID: PMC10512310 DOI: 10.3389/ffunb.2023.1171100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal-methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain Anaeromyces robustus cocultivated with the methanogen Methanobacterium bryantii upregulated genes encoding fungal carbohydrate-active enzymes and other cellulosome components relative to fungal monocultures during this time frame, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. These results demonstrate the importance of establishing methods to extract high-quality RNA from anaerobic fungi at multiple time points during batch cultivation.
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Affiliation(s)
- Jennifer L. Brown
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Taylor Gierke
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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8
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Vigneaud J, Kohler A, Sow MD, Delaunay A, Fauchery L, Guinet F, Daviaud C, Barry KW, Keymanesh K, Johnson J, Singan V, Grigoriev I, Fichot R, Conde D, Perales M, Tost J, Martin FM, Allona I, Strauss SH, Veneault-Fourrey C, Maury S. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. New Phytol 2023; 238:2561-2577. [PMID: 36807327 DOI: 10.1111/nph.18734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.
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Affiliation(s)
- Julien Vigneaud
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Annegret Kohler
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Mamadou Dia Sow
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Laure Fauchery
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Frederic Guinet
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Kerrie W Barry
- 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
| | - Vasanth Singan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor 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
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Francis M Martin
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
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9
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Gupta YK, Marcelino-Guimarães FC, Lorrain C, Farmer A, Haridas S, Ferreira EGC, Lopes-Caitar VS, Oliveira LS, Morin E, Widdison S, Cameron C, Inoue Y, Thor K, Robinson K, Drula E, Henrissat B, LaButti K, Bini AMR, Paget E, Singan V, Daum C, Dorme C, van Hoek M, Janssen A, Chandat L, Tarriotte Y, Richardson J, Melo BDVA, Wittenberg AHJ, Schneiders H, Peyrard S, Zanardo LG, Holtman VC, Coulombier-Chauvel F, Link TI, Balmer D, Müller AN, Kind S, Bohnert S, Wirtz L, Chen C, Yan M, Ng V, Gautier P, Meyer MC, Voegele RT, Liu Q, Grigoriev IV, Conrath U, Brommonschenkel SH, Loehrer M, Schaffrath U, Sirven C, Scalliet G, Duplessis S, van Esse HP. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nat Commun 2023; 14:1835. [PMID: 37005409 PMCID: PMC10067951 DOI: 10.1038/s41467-023-37551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/04/2023] Open
Abstract
With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
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Affiliation(s)
- Yogesh K Gupta
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Cécile Lorrain
- Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Everton Geraldo Capote Ferreira
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Valéria S Lopes-Caitar
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Liliane Santana Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | | | - Connor Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Yoshihiro Inoue
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kathrin Thor
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kelly Robinson
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Elodie Drula
- AFMB, Aix-Marseille Univ., INRAE, Marseille, France
- Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aline Mara Rudsit Bini
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | - Eric Paget
- Bayer SAS, Crop Science Division, Lyon, France
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tobias I Link
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - André N Müller
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Sabine Kind
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Stefan Bohnert
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Louisa Wirtz
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Maurício Conrado Meyer
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | | | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | - Marco Loehrer
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | | | | | - H Peter van Esse
- 2Blades, Evanston, Illinois, USA.
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
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10
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Stuart EK, Singan V, Amirebrahimi M, Na H, Ng V, Grigoriev I, Martin F, Anderson IC, Plett JM, Plett KL. Acquisition of host-derived carbon in biomass of ectomycorrhizal fungus pisolithus microcarpus is correlated to fungal carbon demand and plant defences. FEMS Microbiol Ecol 2023; 99:7098302. [PMID: 37002370 DOI: 10.1093/femsec/fiad037] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Abstract
Ectomycorrhizal (ECM) fungi are key players in forest carbon (C) sequestration, receiving a substantial proportion of photosynthetic C from their forest tree hosts in exchange for plant growth-limiting soil nutrients. However, it remains unknown whether the fungus or plant controls the quantum of C in this exchange, nor what mechanisms are involved. Here, we aimed to identify physiological and genetic properties of both partners that influence ECM C transfer. Using a microcosm system, stable isotope tracing, and transcriptomics, we quantified plant-to-fungus C transfer between the host plant Eucalyptus grandis and nine isolates of the ECM fungus Pisolithus microcarpus that range in their mycorrhization potential and investigated fungal growth characteristics and plant and fungal genes that correlated with C acquisition. We found that C acquisition by P. microcarpus correlated positively with both fungal biomass production and the expression of a subset of fungal C metabolism genes. In the plant, C transfer was not positively correlated to the number of colonised root tips, but rather to the expression of defence- and stress-related genes. These findings suggest that C acquisition by ECM fungi involves individual fungal demand for C and defence responses of the host against C drain.
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Affiliation(s)
- Emiko K Stuart
- Hawkesbury Institute for the Environment, Western Sydney University , Richmond, NSW, 2753 Australia
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 USA
| | - Igor Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California , Berkeley, CA 94720 USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE , INRAE GrandEst-Nancy, Champenoux, 54280 France
| | - 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
| | - Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University , Richmond, NSW, 2753 Australia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries , Menangle, NSW, 2568 Australia
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11
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Plett JM, Miyauchi S, Morin E, Plett K, Wong-Bajracharya J, de Freitas Pereira M, Kuo A, Henrissat B, Drula E, Wojtalewicz D, Riley R, Pangilinan J, Andreopoulos W, LaButti K, Daum C, Yoshinaga Y, Fauchery L, Ng V, Lipzen A, Barry K, Singan V, Guo J, Lebel T, Costa MD, Grigoriev IV, Martin F, Anderson IC, Kohler A. Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus. Mol Biol Evol 2023; 40:7051143. [PMID: 36811946 PMCID: PMC10066745 DOI: 10.1093/molbev/msad045] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 12/01/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
The mutualistic ectomycorrhizal (ECM) fungal genus Pisolithus comprises 19 species defined to date which colonize the roots of >50 hosts worldwide suggesting that substantial genomic and functional evolution occurred during speciation. To better understand this intra-genus variation, we undertook a comparative multi-omic study of nine Pisolithus species sampled from North America, South America, Asia, and Australasia. We found that there was a small core set of genes common to all species (13%), and that these genes were more likely to be significantly regulated during symbiosis with a host than accessory or species-specific genes. Thus, the genetic "toolbox" foundational to the symbiotic lifestyle in this genus is small. Transposable elements were located significantly closer to gene classes including effector-like small secreted proteins (SSPs). Poorly conserved SSPs were more likely to be induced by symbiosis, suggesting that they may be a class of protein that tune host specificity. The Pisolithus gene repertoire is characterized by divergent CAZyme profiles when compared with other fungi, both symbiotic and saprotrophic. This was driven by differences in enzymes associated with symbiotic sugar processing, although metabolomic analysis suggest that neither copy number nor expression of these genes is sufficient to predict sugar capture from a host plant or its metabolism in fungal hyphae. Our results demonstrate that intra-genus genomic and functional diversity within ECM fungi is greater than previously thought, underlining the importance of continued comparative studies within the fungal tree of life to refine our focus on pathways and evolutionary processes foundational to this symbiotic lifestyle.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France.,Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany.,Evolution and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
| | - Krista Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia.,Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, Australia
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia.,Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, Australia
| | | | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France.,INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Dominika Wojtalewicz
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Laure Fauchery
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jie Guo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Teresa Lebel
- Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, Australia
| | - Mauricio Dutra Costa
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil.,Laboratório de Associações Micorrízicas, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Av. P. H. Rolfs, s/n, Campus UFV. Bolsista Pesquisador do Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil, Viçosa, Brazil
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA.,Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA
| | - Francis Martin
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Australia
| | - Annegret Kohler
- Université de Lorraine, INRAE, Interactions Arbres/Microorganismes, Champenoux, France
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12
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Brown JL, Perisin MA, Swift CL, Benyamin M, Liu S, Singan V, Zhang Y, Savage E, Pennacchio C, Grigoriev IV, O'Malley MA. Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose. J Ind Microbiol Biotechnol 2022; 49:6823545. [PMID: 36367297 PMCID: PMC9923384 DOI: 10.1093/jimb/kuac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established based on lactate cross-feeding to produce butyrate and butanol from plant biomass. Several co-culture formulations were assembled that consisted of anaerobic fungi (Anaeromyces robustus, Neocallimastix californiae, or Caecomyces churrovis) with the bacterium Clostridium acetobutylicum. Co-cultures were grown simultaneously (e.g., 'one pot'), and compared to cultures where bacteria were cultured in fungal hydrolysate sequentially. Fungal hydrolysis of lignocellulose resulted in 7-11 mM amounts of glucose and xylose, as well as acetate, formate, ethanol, and lactate to support clostridial growth. Under these conditions, one-stage simultaneous co-culture of anaerobic fungi with C. acetobutylicum promoted the production of butyrate up to 30 mM. Alternatively, two-stage growth slightly promoted solventogenesis and elevated butanol levels (∼4-9 mM). Transcriptional regulation in the two-stage growth condition indicated that this cultivation method may decrease the time required to reach solventogenesis and induce the expression of cellulose-degrading genes in C. acetobutylicum due to relieved carbon-catabolite repression. Overall, this study demonstrates a proof of concept for biobutanol and bio-butyrate production from lignocellulose using an anaerobic fungal-bacterial co-culture system.
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Affiliation(s)
- Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Rm 3357 Engineering II, Santa Barbara, CA 93117, USA
| | - Matthew A Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Rm 3357 Engineering II, Santa Barbara, CA 93117, USA
| | - Marcus Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Sanchao Liu
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christa Pennacchio
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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13
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Calhoun S, Kamel B, Bell TA, Kruse CP, Riley R, Singan V, Kunde Y, Gleasner CD, Chovatia M, Sandor L, Daum C, Treen D, Bowen BP, Louie KB, Northen TR, Starkenburg SR, Grigoriev IV. Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Michel KJ, Lima DC, Hundley H, Singan V, Yoshinaga Y, Daum C, Barry K, Broman KW, Buell CR, de Leon N, Kaeppler SM. Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population. Genetics 2022; 221:6571196. [PMID: 35441688 PMCID: PMC9157087 DOI: 10.1093/genetics/iyac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/08/2022] [Indexed: 11/12/2022] Open
Abstract
The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930's. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a six parent multiparent advanced generation intercross (MAGIC) population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in two field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to two testers, respectively, and evaluated as hybrids in two locations in 2018 and 2019 using an incomplete block design. Markers were derived from a Practical Haplotype Graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and two sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55 to 0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49 to 0.55). Overall, this finding is consistent with the overlapping and non-overlapping significant QTL found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.
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Affiliation(s)
- Kathryn J Michel
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dayane C Lima
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hope Hundley
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Vasanth Singan
- Ambry Genetics, 1 Enterprise, Aliso Viejo, CA-92656, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Yuko Yoshinaga
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, California 94720, USA
| | - Karl W Broman
- Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WI 53706, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.,Center for Applied Genetic Technologies, Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.,Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Middleton, WI 53562, USA
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15
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Brown JL, Swift CL, Mondo SJ, Seppala S, Salamov A, Singan V, Henrissat B, Drula E, Henske JK, Lee S, LaButti K, He G, Yan M, Barry K, Grigoriev IV, O'Malley MA. Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates. Biotechnol Biofuels 2021; 14:234. [PMID: 34893091 PMCID: PMC8665504 DOI: 10.1186/s13068-021-02083-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/19/2021] [Indexed: 05/12/2023]
Abstract
Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal-methanogen physical associations and fungal cell wall development and remodeling.
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Affiliation(s)
- Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susanna Seppala
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elodie Drula
- Architecture Et Fonction Des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
- INRAE USC1408, AFMB, 13009, Marseille, France
| | - John K Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Samantha Lee
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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16
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Yates TB, Feng K, Zhang J, Singan V, Jawdy SS, Ranjan P, Abraham PE, Barry K, Lipzen A, Pan C, Schmutz J, Chen JG, Tuskan GA, Muchero W. The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa. Genome Biol Evol 2021; 13:evab198. [PMID: 34469536 PMCID: PMC8445398 DOI: 10.1093/gbe/evab198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 12/13/2022] Open
Abstract
Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.
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Affiliation(s)
- Timothy B Yates
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chongle Pan
- School of Computer Science and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jin-Gui Chen
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Wellington Muchero
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
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17
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Basso V, Kohler A, Miyauchi S, Singan V, Guinet F, Šimura J, Novák O, Barry KW, Amirebrahimi M, Block J, Daguerre Y, Na H, Grigoriev IV, Martin F, Veneault-Fourrey C. An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots. Plant Cell Environ 2020; 43:1047-1068. [PMID: 31834634 DOI: 10.1111/pce.13702] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. Here, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.
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Affiliation(s)
- Veronica Basso
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Annegret Kohler
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Shingo Miyauchi
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Vasanth Singan
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Frédéric Guinet
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Jan Šimura
- Laboratory of Growth, Palacký University, Faculty of Science & The Czech Academy of Sciences, Institute of Experimental Botany, Olomouc, The Czech Republic
| | - Ondřej Novák
- Laboratory of Growth, Palacký University, Faculty of Science & The Czech Academy of Sciences, Institute of Experimental Botany, Olomouc, The Czech Republic
| | - Kerrie W Barry
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Mojgan Amirebrahimi
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Jonathan Block
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
| | - Yohann Daguerre
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
- Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Umeå, Sweden
| | - Hyunsoo Na
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
| | - Igor V Grigoriev
- Joint Genome Institute (JGI), US Department of Energy, Walnut Creek, California
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California
| | - Francis Martin
- INRA, UMR Interactions Arbres/Microorganismes (IAM), Laboratoire d'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (LabEx ARBRE), Centre INRA Grand-Est, University of Lorraine, Champenoux, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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18
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Zhang J, Xie M, Li M, Ding J, Pu Y, Bryan AC, Rottmann W, Winkeler KA, Collins CM, Singan V, Lindquist EA, Jawdy SS, Gunter LE, Engle NL, Yang X, Barry K, Tschaplinski TJ, Schmutz J, Tuskan GA, Muchero W, Chen J. Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus. Plant Biotechnol J 2020; 18:859-871. [PMID: 31498543 PMCID: PMC7004918 DOI: 10.1111/pbi.13254] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 05/06/2023]
Abstract
Prefoldin (PFD) is a group II chaperonin that is ubiquitously present in the eukaryotic kingdom. Six subunits (PFD1-6) form a jellyfish-like heterohexameric PFD complex and function in protein folding and cytoskeleton organization. However, little is known about its function in plant cell wall-related processes. Here, we report the functional characterization of a PFD gene from Populus deltoides, designated as PdPFD2.2. There are two copies of PFD2 in Populus, and PdPFD2.2 was ubiquitously expressed with high transcript abundance in the cambial region. PdPFD2.2 can physically interact with DELLA protein RGA1_8g, and its subcellular localization is affected by the interaction. In P. deltoides transgenic plants overexpressing PdPFD2.2, the lignin syringyl/guaiacyl ratio was increased, but cellulose content and crystallinity index were unchanged. In addition, the total released sugar (glucose and xylose) amounts were increased by 7.6% and 6.1%, respectively, in two transgenic lines. Transcriptomic and metabolomic analyses revealed that secondary metabolic pathways, including lignin and flavonoid biosynthesis, were affected by overexpressing PdPFD2.2. A total of eight hub transcription factors (TFs) were identified based on TF binding sites of differentially expressed genes in Populus transgenic plants overexpressing PdPFD2.2. In addition, several known cell wall-related TFs, such as MYB3, MYB4, MYB7, TT8 and XND1, were affected by overexpression of PdPFD2.2. These results suggest that overexpression of PdPFD2.2 can reduce biomass recalcitrance and PdPFD2.2 is a promising target for genetic engineering to improve feedstock characteristics to enhance biofuel conversion and reduce the cost of lignocellulosic biofuel production.
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Affiliation(s)
- Jin Zhang
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Meng Xie
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Mi Li
- Chemical & Biomolecular EngineeringUniversity of TennesseeKnoxvilleTNUSA
| | - Jinhua Ding
- Chemical & Biomolecular EngineeringUniversity of TennesseeKnoxvilleTNUSA
- College of TextilesDonghua UniversityShanghaiChina
| | - Yunqiao Pu
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | | | | | - Vasanth Singan
- U.S. Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | | | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Lee E. Gunter
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Xiaohan Yang
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Timothy J. Tschaplinski
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome InstituteWalnut CreekCAUSA
- HudsonAlpha Institute for BiotechnologyHuntsvilleALUSA
| | - Gerald A. Tuskan
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Wellington Muchero
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTNUSA
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19
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Kowalczyk JE, Peng M, Pawlowski M, Lipzen A, Ng V, Singan V, Wang M, Grigoriev IV, Mäkelä MR. The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds. Front Bioeng Biotechnol 2019; 7:229. [PMID: 31616664 PMCID: PMC6763618 DOI: 10.3389/fbioe.2019.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/05/2019] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic plant biomass is an important feedstock for bio-based economy. In particular, it is an abundant renewable source of aromatic compounds, which are present as part of lignin, as side-groups of xylan and pectin, and in other forms, such as tannins. As filamentous fungi are the main organisms that modify and degrade lignocellulose, they have developed a versatile metabolism to convert the aromatic compounds that are toxic at relatively low concentrations to less toxic ones. During this process, fungi form metabolites some of which represent high-value platform chemicals or important chemical building blocks, such as benzoic, vanillic, and protocatechuic acid. Especially basidiomycete white-rot fungi with unique ability to degrade the recalcitrant lignin polymer are expected to perform highly efficient enzymatic conversions of aromatic compounds, thus having huge potential for biotechnological exploitation. However, the aromatic metabolism of basidiomycete fungi is poorly studied and knowledge on them is based on the combined results of studies in variety of species, leaving the overall picture in each organism unclear. Dichomitus squalens is an efficiently wood-degrading white-rot basidiomycete that produces a diverse set of extracellular enzymes targeted for lignocellulose degradation, including oxidative enzymes that act on lignin. Our recent study showed that several intra- and extracellular aromatic compounds were produced when D. squalens was cultivated on spruce wood, indicating also versatile aromatic metabolic abilities for this species. In order to provide the first molecular level systematic insight into the conversion of plant biomass derived aromatic compounds by basidiomycete fungi, we analyzed the transcriptomes of D. squalens when grown with 10 different lignocellulose-related aromatic monomers. Significant differences for example with respect to the expression of lignocellulose degradation related genes, but also putative genes encoding transporters and catabolic pathway genes were observed between the cultivations supplemented with the different aromatic compounds. The results demonstrate that the transcriptional response of D. squalens is highly dependent on the specific aromatic compounds present suggesting that instead of a common regulatory system, fine-tuned regulation is needed for aromatic metabolism.
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Affiliation(s)
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Megan Pawlowski
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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20
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de Freitas Pereira M, Veneault-Fourrey C, Vion P, Guinet F, Morin E, Barry KW, Lipzen A, Singan V, Pfister S, Na H, Kennedy M, Egli S, Grigoriev I, Martin F, Kohler A, Peter M. Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum. Front Microbiol 2018; 9:141. [PMID: 29487573 PMCID: PMC5816826 DOI: 10.3389/fmicb.2018.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/22/2018] [Indexed: 11/21/2022] Open
Abstract
Cenococcum geophilum is an ectomycorrhizal fungus with global distribution in numerous habitats and associates with a large range of host species including gymnosperm and angiosperm trees. Moreover, C. geophilum is the unique ectomycorrhizal species within the clade Dothideomycetes, the largest class of Ascomycetes containing predominantly saprotrophic and many devastating phytopathogenic fungi. Recent studies highlight that mycorrhizal fungi, as pathogenic ones, use effectors in form of Small Secreted Proteins (SSPs) as molecular keys to promote symbiosis. In order to better understand the biotic interaction of C. geophilum with its host plants, the goal of this work was to characterize mycorrhiza-induced small-secreted proteins (MiSSPs) that potentially play a role in the ectomycorrhiza formation and functioning of this ecologically very important species. We combined different approaches such as gene expression profiling, genome localization and conservation of MiSSP genes in different C. geophilum strains and closely related species as well as protein subcellular localization studies of potential targets of MiSSPs in interacting plants using in tobacco leaf cells. Gene expression analyses of C. geophilum interacting with Pinus sylvestris (pine) and Populus tremula × Populus alba (poplar) showed that similar sets of genes coding for secreted proteins were up-regulated and only few were specific to each host. Whereas pine induced more carbohydrate active enzymes (CAZymes), the interaction with poplar induced the expression of specific SSPs. We identified a set of 22 MiSSPs, which are located in both, gene-rich, repeat-poor or gene-sparse, repeat-rich regions of the C. geophilum genome, a genome showing a bipartite architecture as seen for some pathogens but not yet for an ectomycorrhizal fungus. Genome re-sequencing data of 15 C. geophilum strains and two close relatives Glonium stellatum and Lepidopterella palustris were used to study sequence conservation of MiSSP-encoding genes. The 22 MiSSPs showed a high presence-absence polymorphism among the studied C. geophilum strains suggesting an evolution through gene gain/gene loss. Finally, we showed that six CgMiSSPs target four distinct sub-cellular compartments such as endoplasmic reticulum, plasma membrane, cytosol and tonoplast. Overall, this work presents a comprehensive analysis of secreted proteins and MiSSPs in different genetic level of C. geophilum opening a valuable resource to future functional analysis.
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Affiliation(s)
- Maíra de Freitas Pereira
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
- Swiss Federal Research Institute WSL, Forest Dynamics, Birmensdorf, Switzerland
| | - Claire Veneault-Fourrey
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
- Université de Lorraine, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, Vandoeuvre les Nancy, France
| | - Patrice Vion
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
| | - Fréderic Guinet
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
- Université de Lorraine, Unité Mixte de Recherche 1136 Interactions Arbres-Microorganismes, Vandoeuvre les Nancy, France
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
| | - Kerrie W. Barry
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vasanth Singan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Stephanie Pfister
- Swiss Federal Research Institute WSL, Forest Dynamics, Birmensdorf, Switzerland
| | - Hyunsoo Na
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Megan Kennedy
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Simon Egli
- Swiss Federal Research Institute WSL, Forest Dynamics, Birmensdorf, Switzerland
| | - Igor Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Francis Martin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
| | - Annegret Kohler
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres, Microorganismes, Laboratoire D'excellence Recherches Avancés sur la Biologie de l'Arbre et les Ecosystémes Forestiers, Centre Institut National de la Recherche Agronomique-Lorraine, Champenoux, France
| | - Martina Peter
- Swiss Federal Research Institute WSL, Forest Dynamics, Birmensdorf, Switzerland
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Castanera R, Pérez G, López-Varas L, Amselem J, LaButti K, Singan V, Lipzen A, Haridas S, Barry K, Grigoriev IV, Pisabarro AG, Ramírez L. Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales. BMC Genomics 2017; 18:883. [PMID: 29145801 PMCID: PMC5689174 DOI: 10.1186/s12864-017-4243-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/31/2017] [Indexed: 12/13/2022] Open
Abstract
Background Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. Results In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years. Conclusions Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4243-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain
| | - Gúmer Pérez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain
| | - Leticia López-Varas
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain
| | - Joëlle Amselem
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Kurt LaButti
- U.S.Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Vasanth Singan
- U.S.Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- U.S.Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Sajeet Haridas
- U.S.Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- U.S.Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- U.S.Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Navarre, Spain.
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Doré J, Kohler A, Dubost A, Hundley H, Singan V, Peng Y, Kuo A, Grigoriev IV, Martin F, Marmeisse R, Gay G. The ectomycorrhizal basidiomyceteHebeloma cylindrosporumundergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation. Environ Microbiol 2017; 19:1338-1354. [DOI: 10.1111/1462-2920.13670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Jeanne Doré
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
| | - Annegret Kohler
- Interactions Arbres/Microorganismes, INRA-Nancy; INRA, UMR 1136 INRA-Université de Lorraine; Champenoux 54280 France
| | - Audrey Dubost
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
| | - Hope Hundley
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Yi Peng
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - Francis Martin
- Interactions Arbres/Microorganismes, INRA-Nancy; INRA, UMR 1136 INRA-Université de Lorraine; Champenoux 54280 France
| | - Roland Marmeisse
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
| | - Gilles Gay
- Ecologie Microbienne; Université de Lyon; F-69622 Lyon France
- Université Lyon 1, CNRS, UMR5557, INRA, UMR1418; Villeurbanne France
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Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A 2007; 104:10376-81. [PMID: 17563368 PMCID: PMC1965521 DOI: 10.1073/pnas.0700962104] [Citation(s) in RCA: 383] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Indexed: 11/18/2022] Open
Abstract
Recent fermentation studies have identified actinomycetes of the marine-dwelling genus Salinispora as prolific natural product producers. To further evaluate their biosynthetic potential, we sequenced the 5,183,331-bp S. tropica CNB-440 circular genome and analyzed all identifiable secondary natural product gene clusters. Our analysis shows that S. tropica dedicates a large percentage of its genome ( approximately 9.9%) to natural product assembly, which is greater than previous Streptomyces genome sequences as well as other natural product-producing actinomycetes. The S. tropica genome features polyketide synthase systems of every known formally classified family, nonribosomal peptide synthetases, and several hybrid clusters. Although a few clusters appear to encode molecules previously identified in Streptomyces species, the majority of the 17 biosynthetic loci are novel. Specific chemical information about putative and observed natural product molecules is presented and discussed. In addition, our bioinformatic analysis not only was critical for the structure elucidation of the polyene macrolactam salinilactam A, but its structural analysis aided the genome assembly of the highly repetitive slm loci. This study firmly establishes the genus Salinispora as a rich source of drug-like molecules and importantly reveals the powerful interplay between genomic analysis and traditional natural product isolation studies.
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Affiliation(s)
| | | | | | - Vasanth Singan
- Department of Energy, Joint Genome Institute–Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598
| | - Alla Lapidus
- Department of Energy, Joint Genome Institute–Lawrence Berkeley National Laboratory, Walnut Creek, CA 94598
| | | | | | - Bradley S. Moore
- *Scripps Institution of Oceanography and
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093-0204; and
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