1
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Leavitt SD, DeBolt A, McQuhae E, Allen JL. Genomic Resources for the First Federally Endangered Lichen: The Florida Perforate Cladonia ( Cladonia perforata). J Fungi (Basel) 2023; 9:698. [PMID: 37504687 PMCID: PMC10381751 DOI: 10.3390/jof9070698] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/29/2023] Open
Abstract
Thirty years after its designation as a federally endangered species, the Florida Perforate Cladonia (FPC) remains imperiled in isolated populations in the Florida scrub in the southeastern USA. For threatened and endangered species, such as FPC, reference genomes provide critical insight into genomic diversity, local adaptations, landscape-level genetics, and phylogenomics. Using high-throughput sequencing, we assemble the first draft nuclear and mitochondrial genomes for the FPC mycobiont-Cladonia perforata. We also assess genetic diversity within and among populations in southeastern Florida using genome-scale data and investigate diversity across the entire nuclear ribosomal cistron, including the standard DNA barcoding marker for fungi. The draft nuclear genome spanned 33.6 Mb, and the complete, circular mitochondrial genome was 59 Kb. We also generated the first chloroplast genome, to our knowledge, for the photobiont genus associated with FPC, an undescribed Asterochloris species. We inferred the presence of multiple, distinct mycobiont parental genotypes (genets) occurring at local scales in southeastern Florida, and strikingly, no genets were shared among even the closest sample sites. All sampled thalli shared identical mitochondrial genomes, while the nuclear ribosomal cistron showed limited variability-highlighting the genetic resolution provided by nuclear genome-scale datasets. The genomic resources generated here provide critical resources for informed conservation efforts for the FPC.
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Affiliation(s)
- Steven D Leavitt
- M.L. Bean Life Science Museum and Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Ann DeBolt
- Department of Biology, Boise State University, Boise, ID 83725, USA
| | - Ethan McQuhae
- Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Jessica L Allen
- Department of Biology, Eastern Washington University, Cheney, WA 99004, USA
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2
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Paguirigan JAG, Kim JA, Hur JS, Kim W. Identification of a biosynthetic gene cluster for a red pigment cristazarin produced by a lichen-forming fungus Cladonia metacorallifera. PLoS One 2023; 18:e0287559. [PMID: 37352186 PMCID: PMC10289310 DOI: 10.1371/journal.pone.0287559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
Lichens are known to produce many novel bioactive metabolites. To date, approximately 1,000 secondary metabolites have been discovered, which are predominantly produced by the lichen mycobionts. However, despite the extensive studies on production of lichen secondary metabolites, little is known about the responsible biosynthetic gene clusters (BGCs). Here, we identified a putative BGC that is implicated in production of a red pigment, cristazarin (a naphthazarin derivative), in Cladonia metacorallifera. Previously, cristazarin was shown to be specifically induced in growth media containing fructose as a sole carbon source. Thus, we performed transcriptome analysis of C. metacorallifera growing on different carbon sources including fructose to identify the BGC for cristazarin. Among 39 polyketide synthase (PKS) genes found in the genome of C. metacorallifera, a non-reducing PKS (coined crz7) was highly expressed in growth media containing either fructose or glucose. The borders of a cristazarin gene cluster were delimited by co-expression patterns of neighboring genes of the crz7. BGCs highly conserved to the cristazarin BGC were also found in C. borealis and C. macilenta, indicating that these related species also have metabolic potentials to produce cristazarin. Phylogenetic analysis revealed that the Crz7 is sister to fungal PKSs that biosynthesize an acetylated tetrahydoxynaphthalene as a precursor of melanin pigment. Based on the phylogenetic placement of the Crz7 and putative functions of its neighboring genes, we proposed a plausible biosynthetic route for cristazarin. In this study, we identified a lichen-specific BGC that is likely involved in the biosynthesis of a naphthazarin derivative, cristazarin, and confirmed that transcriptome profiling under inducing and non-inducing conditions is an effective strategy for linking metabolites of interest to biosynthetic genes.
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Affiliation(s)
- Jaycee Augusto Gumiran Paguirigan
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Jung A. Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
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3
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A comparative genomic analysis of lichen-forming fungi reveals new insights into fungal lifestyles. Sci Rep 2022; 12:10724. [PMID: 35750715 PMCID: PMC9232553 DOI: 10.1038/s41598-022-14340-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Lichen-forming fungi are mutualistic symbionts of green algae or cyanobacteria. We report the comparative analysis of six genomes of lichen-forming fungi in classes Eurotiomycetes and Lecanoromycetes to identify genomic information related to their symbiotic lifestyle. The lichen-forming fungi exhibited genome reduction via the loss of dispensable genes encoding plant-cell-wall-degrading enzymes, sugar transporters, and transcription factors. The loss of these genes reflects the symbiotic biology of lichens, such as the absence of pectin in the algal cell wall and obtaining specific sugars from photosynthetic partners. The lichens also gained many lineage- and species-specific genes, including those encoding small secreted proteins. These genes are primarily induced during the early stage of lichen symbiosis, indicating their significant roles in the establishment of lichen symbiosis.Our findings provide comprehensive genomic information for six lichen-forming fungi and novel insights into lichen biology and the evolution of symbiosis.
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4
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Duong TA, Aylward J, Ametrano CG, Poudel B, Santana QC, Wilken PM, Martin A, Arun-Chinnappa KS, de Vos L, DiStefano I, Grewe F, Huhndorf S, Lumbsch HT, Rakoma JR, Poudel B, Steenkamp ET, Sun Y, van der Nest MA, Wingfield MJ, Yilmaz N, Wingfield BD. IMA Genome - F15 : Draft genome assembly of Fusarium pilosicola, Meredithiella fracta, Niebla homalea, Pyrenophora teres hybrid WAC10721, and Teratosphaeria viscida. IMA Fungus 2021; 12:30. [PMID: 34645521 PMCID: PMC8513234 DOI: 10.1186/s43008-021-00077-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Tuan Anh Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Claudio Gennaro Ametrano
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Barsha Poudel
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Quentin Carlo Santana
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pieter Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Kiruba Shankari Arun-Chinnappa
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
- PerkinElmer Pty LTD., Level 2, Building 5, Brandon Business Park 530-540, Springvale Road, Glen Waverley, VIC, 3150, Australia
| | - Lieschen de Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Isabel DiStefano
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Felix Grewe
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Sabine Huhndorf
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Helge Thorsten Lumbsch
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Jostina Raesetsa Rakoma
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Barsha Poudel
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Emma Theodora Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Yukun Sun
- Field Museum, Department of Science and Education, Grainger Bioinformatics Center, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa
| | - Michael John Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Neriman Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Brenda Diana Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
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Jeong MH, Park CH, Kim JA, Choi ED, Kim S, Hur JS, Park SY. Production and Activity of Cristazarin in the Lichen-Forming Fungus Cladonia metacorallifera. J Fungi (Basel) 2021; 7:601. [PMID: 34436140 PMCID: PMC8397021 DOI: 10.3390/jof7080601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/18/2022] Open
Abstract
Lichens are a natural source of bioactive compounds. Cladonia metacorallifera var. reagens KoLRI002260 is a rare lichen known to produce phenolic compounds, such as rhodocladonic, thamnolic, and didymic acids. However, these metabolites have not been detected in isolated mycobionts. We investigated the effects of six carbon sources on metabolite biosynthesis in the C. metacorallifera mycobiont. Red pigments appeared only in Lilly and Barnett's media with fructose at 15 °C after 3 weeks of culture and decreased after 6 weeks. We purified these red pigments using preparative-scale high performance liquid chromatography and analyzed them via nuclear magnetic resonance. Results indicated that 1% fructose-induced cristazarin and 6-methylcristazarin production under light conditions. In total, 27 out of 30 putative polyketide synthase genes were differentially expressed after 3 weeks of culture, implying that these genes may be required for cristazarin production in C. metacorallifera. Moreover, the white collar genes Cmwc-1 and Cmwc-2 were highly upregulated at all times under light conditions, indicating a possible correlation between cristazarin production and gene expression. The cancer cell lines AGS, CT26, and B16F1 were sensitive to cristazarin, with IC50 values of 18.2, 26.1, and 30.9 μg/mL, respectively, which highlights the value of cristazarin. Overall, our results suggest that 1% fructose under light conditions is required for cristazarin production by C. metacorallifera mycobionts, and cristazarin could be a good bioactive compound.
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Affiliation(s)
- Min-Hye Jeong
- Korean Lichen Research Institute, Sunchon National University, Sunchoeon 57922, Korea; (M.-H.J.); (C.-H.P.)
- Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea;
| | - Chan-Ho Park
- Korean Lichen Research Institute, Sunchon National University, Sunchoeon 57922, Korea; (M.-H.J.); (C.-H.P.)
| | - Jung A Kim
- National Institute of Biological Resources, Incheon 22689, Korea; (J.A.K.); (S.K.)
| | - Eu Ddeum Choi
- Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea;
| | - Soonok Kim
- National Institute of Biological Resources, Incheon 22689, Korea; (J.A.K.); (S.K.)
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchoeon 57922, Korea; (M.-H.J.); (C.-H.P.)
| | - Sook-Young Park
- Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea;
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6
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Shishido TK, Wahlsten M, Laine P, Rikkinen J, Lundell T, Auvinen P. Microbial Communities of Cladonia Lichens and Their Biosynthetic Gene Clusters Potentially Encoding Natural Products. Microorganisms 2021; 9:1347. [PMID: 34206222 PMCID: PMC8304397 DOI: 10.3390/microorganisms9071347] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.
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Affiliation(s)
- Tânia Keiko Shishido
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (M.W.); (T.L.)
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
| | - Jouko Rikkinen
- Finnish Museum of Natural History, Botany Unit, University of Helsinki, P.O. Box 7, 00014 Helsinki, Finland;
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (M.W.); (T.L.)
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland; (P.L.); (P.A.)
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7
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Nazem-Bokaee H, Hom EFY, Warden AC, Mathews S, Gueidan C. Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling. Front Microbiol 2021; 12:667864. [PMID: 34012428 PMCID: PMC8126723 DOI: 10.3389/fmicb.2021.667864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at the molecular level. This review addresses opportunities for expanding current knowledge on signalling and metabolic interplays in the lichen symbiosis using the tools and approaches of systems biology, particularly network modelling. The largely unexplored nature of symbiont recognition and metabolic interdependency in lichens could benefit from applying a holistic approach to understand underlying molecular mechanisms and processes. Together with ‘omics’ approaches, the application of signalling and metabolic network modelling could provide predictive means to gain insights into lichen signalling and metabolic pathways. First, we review the major signalling and recognition modalities in the lichen symbioses studied to date, and then describe how modelling signalling networks could enhance our understanding of symbiont recognition, particularly leveraging omics techniques. Next, we highlight the current state of knowledge on lichen metabolism. We also discuss metabolic network modelling as a tool to simulate flux distribution in lichen metabolic pathways and to analyse the co-dependence between symbionts. This is especially important given the growing number of lichen genomes now available and improved computational tools for reconstructing such models. We highlight the benefits and possible bottlenecks for implementing different types of network models as applied to the study of lichens.
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Affiliation(s)
- Hadi Nazem-Bokaee
- CSIRO Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, NCMI, Canberra, ACT, Australia.,CSIRO Land and Water, Canberra, ACT, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, The University of Mississippi, University City, MS, United States
| | | | - Sarah Mathews
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Cécile Gueidan
- CSIRO Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, NCMI, Canberra, ACT, Australia
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8
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Erken MT, Cansaran-Duman D, Tanman U. In silico prediction of type I PKS gene modules in nine lichenized fungi. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1879679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
| | - Demet Cansaran-Duman
- System Biotechnology Advance Research Unit, Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Ummugulsum Tanman
- System Biotechnology Advance Research Unit, Biotechnology Institute, Ankara University, Ankara, Turkey
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9
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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10
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McKenzie SK, Walston RF, Allen JL. Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture. Genomics 2020; 112:3150-3156. [PMID: 32504651 DOI: 10.1016/j.ygeno.2020.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
Abstract
Fungal genomes display incredible levels of complexity and diversity, and are exceptional study systems for genome evolution. Here we used the Oxford Nanopore MinION sequencing platform to generate high-quality fungal genomes from complex metagenomic samples of lichen thalli. We sequenced two wolf lichens using one flow cell per sample, generating 17.1 Gbps for Letharia lupina and 14.3 Gbps for Letharia columbiana. The resulting L. lupina genome is one of the most contiguous lichen genomes available to date, with 49.2 Mbp contained on 31 contigs. The L. columbiana genome, while less contiguous, is still relatively high quality, with 52.3 Mbp on a total of 161 contigs. Each thallus for both species contained multiple distinct haplotypes, a phenomenon that has rarely been empirically demonstrated. The Oxford Nanopore sequencing technologies are robust and effective when applied to complex symbioses, and have the potential to fundamentally transform our understanding of fungal genetics.
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Affiliation(s)
- Sean K McKenzie
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Current affiliation: Emory Integrated Computational Core, Emory University, Atlanta, GA, USA.
| | - Ridge F Walston
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Jessica L Allen
- Department of Biology, Eastern Washington University, Cheney, WA, USA
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11
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Roy R, Reinders A, Ward JM, McDonald TR. Understanding transport processes in lichen, Azolla-cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia-legume symbiotic interactions. F1000Res 2020; 9. [PMID: 32047609 PMCID: PMC6979478 DOI: 10.12688/f1000research.19740.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Intimate interactions between photosynthetic and non-photosynthetic organisms require the orchestrated transfer of ions and metabolites between species. We review recent progress in identifying and characterizing the transport proteins involved in five mutualistic symbiotic interactions: lichens,
Azolla–cyanobacteria, ectomycorrhiza, endomycorrhiza, and rhizobia–legumes. This review focuses on transporters for nitrogen and carbon and other solutes exchanged in the interactions. Their predicted functions are evaluated on the basis of their transport mechanism and prevailing transmembrane gradients of H
+ and transported substrates. The symbiotic interactions are presented in the assumed order from oldest to most recently evolved.
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Affiliation(s)
- Rahul Roy
- Department of Plant and Microbial Biology, University of Minnesota, Minnesota, USA
| | - Anke Reinders
- College of Continuing and Professional Studies, University of Minnesota, Minnesota, USA
| | - John M Ward
- Department of Plant and Microbial Biology, University of Minnesota, Minnesota, USA
| | - Tami R McDonald
- Biology Department, St. Catherine University, Minnesota, USA
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12
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Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 2019; 20:605. [PMID: 31337355 PMCID: PMC6652019 DOI: 10.1186/s12864-019-5629-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.
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Affiliation(s)
| | - Olaf Müller
- Department of Biology, Duke University, Durham, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | | | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Guillaume Blanc
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften & Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
| | - Fred Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
| | - Suzanne Joneson
- Department of Biology, Duke University, Durham, USA
- College of General Studies, University of Wisconsin - Milwaukee at Waukesha, Waukesha, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | | | | | - Francis Martin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Susan P. May
- Department of Biology, Duke University, Durham, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, USA
| | - Tami R. McDonald
- Department of Biology, Duke University, Durham, USA
- Department of Biology, St. Catherine University, St. Paul, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, USA
| | - Vivian Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Morin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California - Santa Barbara, Santa Barbara, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, and DOE Institute for Genomics and Proteomics, University of California, Los Angeles, USA
| | - Nimrod Rubinstein
- National Evolutionary Synthesis Center, Durham, USA
- Calico Life Sciences LLC, South San Francisco, USA
| | | | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Fachbereich Biowissenschaften, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason C. Slot
- College of Food, Agricultural, and Environmental Sciences, Department of Plant Pathology, The Ohio State University, Columbus, USA
| | - Darren Soanes
- College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Claire Veneault-Fourrey
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
- Université de Lorraine, INRA, Interactions Arbres-Microorganismes, Faculté des Sciences et Technologies, Vandoeuvre les Nancy Cedex, France
| | - Basil B. Xavier
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J Ind Microbiol Biotechnol 2018; 45:1067-1081. [PMID: 30206732 DOI: 10.1007/s10295-018-2080-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
Lichens are fungi that form symbiotic partnerships with algae. Although lichens produce diverse polyketides, difficulties in establishing and maintaining lichen cultures have prohibited detailed studies of their biosynthetic pathways. Creative, albeit non-definitive, methods have been developed to assign function to biosynthetic gene clusters in lieu of techniques such as gene knockout and heterologous expressions that are commonly applied to easily cultivatable organisms. We review a total of 81 completely sequenced polyketide synthase (PKS) genes from lichenizing fungi, comprising to our best efforts all complete and reported PKS genes in lichenizing fungi to date. This review provides an overview of the approaches used to locate and sequence PKS genes in lichen genomes, current approaches to assign function to lichen PKS gene clusters, and what polyketides are proposed to be biosynthesized by these PKS. We conclude with remarks on prospects for genomics-based natural products discovery in lichens. We hope that this review will serve as a guide to ongoing research efforts on polyketide biosynthesis in lichenizing fungi.
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14
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Wang Y, Geng C, Yuan X, Hua M, Tian F, Li C. Identification of a putative polyketide synthase gene involved in usnic acid biosynthesis in the lichen Nephromopsis pallescens. PLoS One 2018; 13:e0199110. [PMID: 30020937 PMCID: PMC6051580 DOI: 10.1371/journal.pone.0199110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/31/2018] [Indexed: 11/30/2022] Open
Abstract
Usnic acid is a unique polyketide produced by lichens. To characterize usnic acid biosynthesis, the transcriptome of the usnic-acid-producing lichen-forming fungus Nephromopsis pallescens was sequenced using Illumina NextSeq technology. Seven complete non-reducing polyketide synthase genes and nine highly-reducing polyketide synthase genes were obtained through transcriptome analysis. Gene expression results obtained by qPCR and usnic acid detection with LCMS-IT-TOF showed that Nppks7 is probably involved in usnic acid biosynthesis in N. pallescens. Nppks7 is a non-reducing polyketide synthase with a MeT domain that also possesses beta-ketoacyl-ACP synthase, acyl transferase, product template, acyl carrier protein, C-methyltransferase, and Claisen cyclase domains. Phylogenetic analysis shows that Nppks7and other polyketide synthases from lichens form a unique monophyletic clade. Taken together, our data indicate that Nppks7 is a novel PKS in N. pallescens that is likely involved in usnic acid biosynthesis.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming Yunnan, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Changan Geng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiaolong Yuan
- Key Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming Yunnan, China
| | - Mei Hua
- Key Laboratory of Forest Plant Cultivation and Utilization, Yunnan Academy of Forestry, Kunming Yunnan, China
| | - Fenghua Tian
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Changtian Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
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15
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Draft Genome Sequence of the Lichen-Forming Fungus Ramalina intermedia Strain YAF0013. GENOME ANNOUNCEMENTS 2018; 6:6/23/e00478-18. [PMID: 29880593 PMCID: PMC5992360 DOI: 10.1128/genomea.00478-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we report a draft genome sequence of Ramalina intermedia strain YAF0013. The functional annotation of R. intermedia provides important information related to its ability to produce secondary metabolites. The genome sequence reported here builds the basis for further genome mining.
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Wang Y, Wei X, Huang J, Wei J. Modification and functional adaptation of the MBF1 gene family in the lichenized fungus Endocarpon pusillum under environmental stress. Sci Rep 2017; 7:16333. [PMID: 29180801 PMCID: PMC5703946 DOI: 10.1038/s41598-017-16716-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
The multiprotein-bridging factor 1 (MBF1) gene family is well known in archaea, non-lichenized fungi, plants, and animals, and contains stress tolerance-related genes. Here, we identified four unique mbf1 genes in the lichenized fungi Endocarpon spp. A phylogenetic analysis based on protein sequences showed the translated MBF1 proteins of the newly isolated mbf1 genes formed a monophyletic clade different from other lichen-forming fungi and Ascomycota groups in general, which may reflect the evolution of the biological functions of MBF1s. In contrast to the lack of function reported in yeast, we determined that lysine114 in the deduced Endocarpon pusillum MBF1 protein (EpMBF1) had a specific function that was triggered by environmental stress. Further, the Endocarpon-specific C-terminus of EpMBF1 was found to participate in stress tolerance. Epmbf1 was induced by a number of abiotic stresses in E. pusillum and transgenic yeast, and its stress-resistant ability was stronger than that of the yeast mbf1. These findings highlight the evolution and function of EpMBF1 and provide new insights into the co-evolution hypothesis of MBF1 and TATA-box-binding proteins.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 10010, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 10010, China.
| | - Jenpan Huang
- Science & Education, The Field Museum, Chicago, IL, 60605, USA
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 10010, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Abstract
ABSTRACT
Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.
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18
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Identification of the Sfp-Type PPTase EppA from the Lichenized Fungus Evernia prunastri. PLoS One 2016; 11:e0145624. [PMID: 26784935 PMCID: PMC4718654 DOI: 10.1371/journal.pone.0145624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/07/2015] [Indexed: 01/12/2023] Open
Abstract
In the last decades, natural products from lichens have gained more interest for pharmaceutical application due to the broad range of their biological activity. However, isolation of the compounds of interest directly from the lichen is neither feasible nor sustainable due to slow growth of many lichens. In order to develop a pipeline for heterologous expression of lichen biosynthesis gene clusters and thus the sustainable production of their bioactive compounds we have identified and characterized the phosphopantheteinyl transferase (PPTase) EppA from the lichen Evernia prunastri. The Sfp-type PPTase EppA was functionally characterized through heterologous expression in E. coli using the production of the blue pigment indigoidine as readout and by complementation of a lys5 deletion in S. cerevisiae.
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