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Ángeles-Argáiz RE, Aguirre-Beltrán LFL, Hernández-Oaxaca D, Quintero-Corrales C, Trujillo-Roldán MA, Castillo-Ramírez S, Garibay-Orijel R. Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly. Microb Genom 2024; 10:001218. [PMID: 38529901 PMCID: PMC10995626 DOI: 10.1099/mgen.0.001218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/01/2024] [Indexed: 03/27/2024] Open
Abstract
Genome assembly and annotation using short-paired reads is challenging for eukaryotic organisms due to their large size, variable ploidy and large number of repetitive elements. However, the use of single-molecule long reads improves assembly quality (completeness and contiguity), but haplotype duplications still pose assembly challenges. To address the effect of read length on genome assembly quality, gene prediction and annotation, we compared genome assemblers and sequencing technologies with four strains of the ectomycorrhizal fungus Laccaria trichodermophora. By analysing the predicted repertoire of carbohydrate enzymes, we investigated the effects of assembly quality on functional inferences. Libraries were generated using three different sequencing platforms (Illumina Next-Seq, Mi-Seq and PacBio Sequel), and genomes were assembled using single and hybrid assemblies/libraries. Long reads or hybrid assemby resolved the collapsing of repeated regions, but the nuclear heterozygous versions remained unresolved. In dikaryotic fungi, each cell includes two nuclei and each nucleus has differences not only in allelic gene version but also in gene composition and synteny. These heterokaryotic cells produce fragmentation and size overestimation of the genome assembly of each nucleus. Hybrid assembly revealed a wider functional diversity of genomes. Here, several predicted oxidizing activities on glycosyl residues of oligosaccharides and several chitooligosaccharide acetylase activities would have passed unnoticed in short-read assemblies. Also, the size and fragmentation of the genome assembly, in combination with heterozygosity analysis, allowed us to distinguish homokaryotic and heterokaryotic strains isolated from L. trichodermophora fruit bodies.
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Affiliation(s)
- Rodolfo Enrique Ángeles-Argáiz
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de los Posgrados s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Red de Manejo Biotecnológico de Recursos, Instituto de Ecología A. C. Carretera antigua a Coatepec 351, Col. El Haya, Xalapa, Veracruz, México, C.P. 91612, Mexico
| | - Luis Fernando Lozano Aguirre-Beltrán
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62210, Mexico
| | - Diana Hernández-Oaxaca
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62210, Mexico
- Red de Biodiversidad y Sistemática, Instituto de Ecología A. C. Carretera antigua a Coatepec 351, Col. El Haya, Xalapa, Veracruz, México, C.P. 91073, Mexico
| | - Christian Quintero-Corrales
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de los Posgrados s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
| | - Mauricio A. Trujillo-Roldán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera Tijuana-Ensenada, Ensenada, Baja California, Mexico, C.P. 22860, Mexico
| | - Santiago Castillo-Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México, C.P. 62210, Mexico
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Delegación Coyoacán, Ciudad de México, México, C.P. 04510, Mexico
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Oggenfuss U, Badet T, Croll D. A systematic screen for co-option of transposable elements across the fungal kingdom. Mob DNA 2024; 15:2. [PMID: 38245743 PMCID: PMC10799480 DOI: 10.1186/s13100-024-00312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Microbiology and Immunology, University of Minnesota, Medical School, Minneapolis, Minnesota, United States of America
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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Li Q, Luo Y, Sha A, Xiao W, Xiong Z, Chen X, He J, Peng L, Zou L. Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species. Front Microbiol 2023; 14:1134228. [PMID: 36970689 PMCID: PMC10030801 DOI: 10.3389/fmicb.2023.1134228] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/14/2023] [Indexed: 03/10/2023] Open
Abstract
IntroductionCodon basis is a common and complex natural phenomenon observed in many kinds of organisms.MethodsIn the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine Amanita species.ResultsThe results showed that the codons of all Amanita species tended to end in A/T, demonstrating the preference of mitochondrial codons of Amanita species for a preference for this codon. In addition, we detected the correlation between codon base composition and the codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (FOP) indices, indicating the influence of base composition on codon bias. The average effective number of codons (ENC) of mitochondrial core PCGs of Amanita is 30.81, which is <35, demonstrating the strong codon preference of mitochondrial core PCGs of Amanita. The neutrality plot analysis and PR2-Bias plot analysis further demonstrated that natural selection plays an important role in Amanita codon bias. In addition, we obtained 5–10 optimal codons (ΔRSCU > 0.08 and RSCU > 1) in nine Amanita species, and GCA and AUU were the most widely used optimal codons. Based on the combined mitochondrial sequence and RSCU value, we deduced the genetic relationship between different Amanita species and found large variations between them.DiscussionThis study promoted the understanding of synonymous codon usage characteristics and evolution of this important fungal group.
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Kobayashi Y, Shibata TF, Hirakawa H, Nishiyama T, Yamada A, Hasebe M, Shigenobu S, Kawaguchi M. The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. DNA Res 2023; 30:6969780. [PMID: 36610744 PMCID: PMC9896470 DOI: 10.1093/dnares/dsac053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics of mycorrhizal fungi, such as genome size expansion and decreases in plant cell-wall degrading enzymes (PCWDEs). However, genomic changes concerning the evolutionary transition to the ectomycorrhizal lifestyle are largely unknown. In this study, we sequenced the genome of Lyophyllum shimeji, an ectomycorrhizal fungus that is phylogenetically related to saprotrophic species and retains some saprotroph-like traits. We found that the genome of Ly. shimeji strain AT787 lacks both incremental increases in genome size and reduced numbers of PCWDEs. Our findings suggest that the previously reported common genomic traits of mycorrhizal fungi are not essential for the ectomycorrhizal lifestyle, but are a result of abolishing saprotrophic activity. Since Ly. shimeji is commercially consumed as an edible mushroom, the newly available genomic information may also impact research designed to enhance the cultivation of this mushroom.
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Affiliation(s)
- Yuuki Kobayashi
- To whom correspondence should be addressed. Tel.: +81-0564-55-7672, (Y.K.)
| | - Tomoko F Shibata
- Division of Evolutionary Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Akiyoshi Yamada
- Faculty of Agriculture, Shinshu University, Kamiina, Nagano 399-4598, Japan
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan,Department of Basic Biology, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Laboratory of Evolutionary Genomics, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan,Department of Basic Biology, SOKENDAI, Okazaki, Aichi 444-8585, Japan,Trans-omics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
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Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses. PLANTS 2022; 11:plants11151962. [PMID: 35956440 PMCID: PMC9370660 DOI: 10.3390/plants11151962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:6615459. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Corresponding author: Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany. E-mail:
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Corresponding author: Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,
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Zámocký M, Musil M, Danchenko M, Ferianc P, Chovanová K, Baráth P, Poljovka A, Bednář D. Deep Insights into the Specific Evolution of Fungal Hybrid B Heme Peroxidases. BIOLOGY 2022; 11:biology11030459. [PMID: 35336832 PMCID: PMC8945051 DOI: 10.3390/biology11030459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Fungi are well equipped to cope with oxidative stress and the reactive oxygen species that are, in the case of phytopathogens, produced mainly by the plant host for defence purposes. Peroxidases represent the major line of evolution for rapid decomposition of harmful peroxides in all aerobically metabolising organisms. In all the sequenced fungal genomes, many divergent genes coding for various peroxidases have been discovered, and Hybrid B heme peroxidases represent a distinctive mode of fungal-gene evolution within a large peroxidase–catalase superfamily that ranges from bacteria to plants. Abstract In this study, we focus on a detailed bioinformatics analysis of hyBpox genes, mainly within the genomes of Sclerotiniaceae (Ascomycota, Leotiomycetes), which is a specifically evolved fungal family of necrotrophic host generalists and saprophytic or biotrophic host specialists. Members of the genus Sclerotium produce only sclerotia and no fruiting bodies or spores. Thus, their physiological role for peroxidases remains open. A representative species, S. cepivorum, is a dangerous plant pathogen causing white rot in Allium species, particularly in onions, leeks, and garlic. On a worldwide basis, the white rot caused by this soil-borne fungus is apparently the most serious threat to Allium-crop production. We have also found very similar peroxidase sequences in the related fungus S. sclerotiorum, although with minor yet important modifications in the architecture of its active centre. The presence of ScephyBpox1-specific mRNA was confirmed by transcriptomic analysis. The presence of Hybrid B peroxidase at the protein level as the sole extracellular peroxidase of this fungus was confirmed in the secretome of S. cepivorum through detailed proteomic analyses. This prompted us to systematically search for all available genes coding for Hybrid B heme peroxidases in the whole fungal family of Sclerotiniaceae. We present here a reconstruction of their molecular phylogeny and analyse the unique aspects of their conserved-sequence features and structural folds in corresponding ancestral sequences.
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Affiliation(s)
- Marcel Zámocký
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; (P.F.); (K.C.); (A.P.)
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, 1190 Vienna, Austria
- Correspondence: or ; Tel.: +421-2-5930-7481
| | - Miloš Musil
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic; (M.M.); (D.B.)
- International Clinical Research Centre, St. Anne’s University Hospital Brno, CZ-65691 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, CZ-61200 Brno, Czech Republic
| | - Maksym Danchenko
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovakia; (M.D.); (P.B.)
| | - Peter Ferianc
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; (P.F.); (K.C.); (A.P.)
| | - Katarína Chovanová
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; (P.F.); (K.C.); (A.P.)
| | - Peter Baráth
- Department of Glycobiology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovakia; (M.D.); (P.B.)
| | - Andrej Poljovka
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; (P.F.); (K.C.); (A.P.)
| | - David Bednář
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic; (M.M.); (D.B.)
- International Clinical Research Centre, St. Anne’s University Hospital Brno, CZ-65691 Brno, Czech Republic
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Hupperts SF, Lilleskov EA. Predictors of taxonomic and functional composition of black spruce seedling ectomycorrhizal fungal communities along peatland drainage gradients. MYCORRHIZA 2022; 32:67-81. [PMID: 35034180 DOI: 10.1007/s00572-021-01060-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Many trees depend on symbiotic ectomycorrhizal fungi for nutrients in exchange for photosynthetically derived carbohydrates. Trees growing in peatlands, which cover 3% of the earth's terrestrial surface area yet hold approximately one-third of organic soil carbon stocks, may benefit from ectomycorrhizal fungi that can efficiently forage for nutrients and degrade organic matter using oxidative enzymes such as class II peroxidases. However, such traits may place a higher carbon cost on both the fungi and host tree. To investigate these trade-offs that might structure peatland ectomycorrhizal fungal communities, we sampled black spruce (Picea mariana (Mill.)) seedlings along 100-year-old peatland drainage gradients in Minnesota, USA, that had resulted in higher soil nitrogen and canopy density. Structural equation models revealed that the relative abundance of the dominant ectomycorrhizal fungal genus, Cortinarius, which is known for relatively high fungal biomass coupled with elevated class II peroxidase potential, was negatively linked to site fertility but more positively affected by recent host stem radial growth, suggesting carbon limitation. In contrast, Cenococcum, known for comparatively lower fungal biomass and less class II peroxidase potential, was negatively linked to host stem radial growth and unrelated to site fertility. Like Cortinarius, the estimated relative abundance of class II peroxidase genes in the ectomycorrhizal community was more related to host stem radial growth than site fertility. Our findings indicate a trade-off between symbiont foraging traits and associated carbon costs that consequently structure seedling ectomycorrhizal fungal communities in peatlands.
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Affiliation(s)
- Stefan F Hupperts
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | - Erik A Lilleskov
- Forestry Sciences Laboratory, USDA Forest Service, Northern Research Station, Houghton, MI, USA.
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Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021; 11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)69-7542-1856
| | - Véronique Jamilloux
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Nathalie Choisne
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Gregor Rolshausen
- Senckenberg Center for Wildlife Genetics, Clamecystrasse 12, 63571 Gelnhausen, Germany;
| | - Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany;
| | - Meike Schulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Strasse. 9, 60438 Frankfurt am Main, Germany
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Bahram M, Netherway T. Fungi as mediators linking organisms and ecosystems. FEMS Microbiol Rev 2021; 46:6468741. [PMID: 34919672 PMCID: PMC8892540 DOI: 10.1093/femsre/fuab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
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Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
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11
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Draft Genome Sequence of the Ectomycorrhizal Fungus Astraeus odoratus from Northern Thailand. Microbiol Resour Announc 2021; 10:e0004421. [PMID: 34197189 PMCID: PMC8248864 DOI: 10.1128/mra.00044-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We report the draft genome sequence of Astraeus odoratus, an edible ectomycorrhizal fungus from northern Thailand. The assembled genome has a size of 45.1 Mb and 13,403 annotated protein-coding genes. This reference genome will provide a better understanding of the biology of mushroom-forming ectomycorrhizal fungi in the family Diplocystidiaceae.
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12
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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13
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Li Q, He X, Ren Y, Xiong C, Jin X, Peng L, Huang W. Comparative Mitogenome Analysis Reveals Mitochondrial Genome Differentiation in Ectomycorrhizal and Asymbiotic Amanita Species. Front Microbiol 2020; 11:1382. [PMID: 32636830 PMCID: PMC7318869 DOI: 10.3389/fmicb.2020.01382] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 11/19/2022] Open
Abstract
In this present study, we assembled and analyzed the mitogenomes of two asymbiotic and six ectomycorrhizal Amanita species based on next-generation sequencing data. The size of the eight Amanita mitogenomes ranged from 37,341 to 137,428 bp, and we considered introns to be one of the main factors contributing to the size variation of Amanita. The introns of the cox1 gene experienced frequent gain/loss events in Amanita; and the intron position class cox1P386 was lost in the six ectomycorrhizal Amanita species. In addition, ectomycorrhizal Amanita species had more repetitive sequences and fewer intergenic sequences than asymbiotic Amanita species in their mitogenomes. Large-scale gene rearrangements were detected in the Amanita species we tested, including gene displacements and inversions. On the basis of the combined mitochondrial gene set, we reconstructed the phylogenetic relationships of 66 Basidiomycetes. The six ectomycorrhizal Amanita species were of single origin, and the two saprophytic Amanita species formed two distinct clades. This study is the first to elucidate the functions of the mitogenome in the evolution and ecological adaptation of Amanita species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiaohui He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Yuanhang Ren
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
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14
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Liang Y, Lu D, Wang S, Zhao Y, Gao S, Han R, Yu J, Zheng W, Geng J, Hu S. Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:341-351. [PMID: 32561469 PMCID: PMC7801210 DOI: 10.1016/j.gpb.2018.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/18/2018] [Indexed: 12/30/2022]
Abstract
Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a genome assembly of A. cylindracea together with comparative genomics and pathway analyses of Agaricales species. The draft, generated from both next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing platforms to overcome high genetic heterozygosity, is composed of a 56.5 Mb sequence and 15,384 predicted genes. This mushroom possesses a complex reproductive system, including tetrapolar heterothallic and secondary homothallic mechanisms, and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources. Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances, including B vitamins, unsaturated fatty acids, and N-acetylglucosamine. RNA-seq data show that A. cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage, whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis. These results reflect diverse functions of the two anatomical structures of the fruiting body. Our comprehensive genomic and transcriptomic data, as well as preliminary comparative analyses, provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.
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Affiliation(s)
- Yuan Liang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dengxue Lu
- Gansu Academy of Sciences, Lanzhou 730000, China
| | - Sen Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuhui Zhao
- Gansu Academy of Sciences, Lanzhou 730000, China
| | - Shenghan Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rongbing Han
- Gansu Academy of Sciences, Lanzhou 730000, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weili Zheng
- Gansu Academy of Sciences, Lanzhou 730000, China.
| | - Jianing Geng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Min B, Yoon H, Park J, Oh YL, Kong WS, Kim JG, Choi IG. Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements. PLoS One 2020; 15:e0227923. [PMID: 31978083 PMCID: PMC6980582 DOI: 10.1371/journal.pone.0227923] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/02/2020] [Indexed: 12/15/2022] Open
Abstract
Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over "CpG" dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in the hyphae, where symbiotic interactions occur with the hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domains (PF01695) were conserved across taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in the hyphae. Similar to other ectomycorrhizal genomes, the CAZyme gene set was reduced in T. matsutake, including losses in the glycoside hydrolase genes. The T. matsutake genome sequence provides insight into the causes and consequences of genome size inflation.
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Affiliation(s)
- Byoungnam Min
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Hyeokjun Yoon
- School of Life Sciences and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu, Korea
| | - Julius Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Youn-Lee Oh
- Mushroom Research Division, National Institute of Horticulture and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, Korea
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticulture and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, Korea
- * E-mail: (IC); (WK); (JK)
| | - Jong-Guk Kim
- School of Life Sciences and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu, Korea
- * E-mail: (IC); (WK); (JK)
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
- * E-mail: (IC); (WK); (JK)
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16
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Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Transposable elements contribute to fungal genes and impact fungal lifestyle. Sci Rep 2019; 9:4307. [PMID: 30867521 PMCID: PMC6416283 DOI: 10.1038/s41598-019-40965-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
The last decade brought a still growing experimental evidence of mobilome impact on host's gene expression. We systematically analysed genomic location of transposable elements (TEs) in 625 publicly available fungal genomes from the NCBI database in order to explore their potential roles in genome evolution and correlation with species' lifestyle. We found that non-autonomous TEs and remnant copies are evenly distributed across genomes. In consequence, they also massively overlap with regions annotated as genes, which suggests a great contribution of TE-derived sequences to host's coding genome. Younger and potentially active TEs cluster with one another away from genic regions. This non-randomness is a sign of either selection against insertion of TEs in gene proximity or target site preference among some types of TEs. Proteins encoded by genes with old transposable elements insertions have significantly less repeat and protein-protein interaction motifs but are richer in enzymatic domains. However, genes only proximal to TEs do not display any functional enrichment. Our findings show that adaptive cases of TE insertion remain a marginal phenomenon, and the overwhelming majority of TEs are evolving neutrally. Eventually, animal-related and pathogenic fungi have more TEs inserted into genes than fungi with other lifestyles. This is the first systematic, kingdom-wide study concerning mobile elements and their genomic neighbourhood. The obtained results should inspire further research concerning the roles TEs played in evolution and how they shape the life we know today.
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Affiliation(s)
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
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17
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Genome of lethal Lepiota venenata and insights into the evolution of toxin-biosynthetic genes. BMC Genomics 2019; 20:198. [PMID: 30849934 PMCID: PMC6408872 DOI: 10.1186/s12864-019-5575-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/28/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushroom poisoning case in China has led to acquisition of fresh L. venenata fruiting bodies, based on which a draft genome was obtained through PacBio and Illumina sequencing platforms. Toxin-biosynthetic MSDIN family and Porlyl oligopeptidase B (POPB) genes were mined from the genome and used for phylogenetic and statistical studies to gain insights into the evolution of the biosynthetic pathway. RESULTS The analysis of the genome data illustrated that only one MSDIN, named LvAMA1, exits in the genome, along with a POPB gene. No POPA homolog was identified by direct homology searching, however, one additional POP gene, named LvPOPC, was cloned and the gene structure determined. Similar to ApAMA1 in A. phalloides and GmAMA1 in G. marginata, LvAMA1 directly encodes α-amanitin. The two toxin genes were mapped to the draft genome, and the structures analyzed. Furthermore, phylogenetic and statistical analyses were conducted to study the evolution history of the POPB genes. Compared to our previous report, the phylogenetic trees unambiguously showed that a monophyletic POPB lineage clearly conflicted with the species phylogeny. In contrast, phylogeny of POPA genes resembled the species phylogeny. Topology and divergence tests showed that the POPB lineage was robust and these genes exhibited significantly shorter genetic distances than those of the house-keeping rbp2, a characteristic feature of genes with horizontal gene transfer (HGT) background. Consistently, same scenario applied to the only MSDIN, LvAMA1, in the genome. CONCLUSIONS To the best of our knowledge, this is the first reported genome of Lepiota. The analyses of the toxin genes indicate that the cyclic peptides are synthesized through a ribosomal mechanism. The toxin genes, LvAMA1 and LvPOPB, are not in the vicinity of each other. Phylogenetic and evolutionary studies suggest that HGT is the underlining cause for the occurrence of POPB and MSDIN in Amanita, Galerina and Lepiota, which are allocated in three distantly-related families.
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18
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Landi N, Ragucci S, Russo R, Pedone PV, Chambery A, Di Maro A. Structural insights into nucleotide and protein sequence of Ageritin: a novel prototype of fungal ribotoxin. J Biochem 2018; 165:415-422. [DOI: 10.1093/jb/mvy113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/10/2018] [Indexed: 02/02/2023] Open
Affiliation(s)
- Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DISTABIF), University of Campania ‘Luigi Vanvitelli’, Via Vivaldi 43, I Caserta, Italy
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Hess J, Skrede I, Chaib De Mares M, Hainaut M, Henrissat B, Pringle A. Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. Mol Biol Evol 2018; 35:2786-2804. [PMID: 30239843 PMCID: PMC6231487 DOI: 10.1093/molbev/msy179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.
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Affiliation(s)
- Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Maryam Chaib De Mares
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin, Madison, Madison, WI
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20
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Rao S, Sharda S, Oddi V, Nandineni MR. The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum. Front Microbiol 2018; 9:2367. [PMID: 30337918 PMCID: PMC6180176 DOI: 10.3389/fmicb.2018.02367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Saphy Sharda
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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21
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Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. MOLECULAR PLANT PATHOLOGY 2018; 19:2094-2110. [PMID: 29569316 PMCID: PMC6638006 DOI: 10.1111/mpp.12682] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 05/14/2023]
Abstract
Plant-pathogenic fungi secrete effector proteins to facilitate infection. We describe extensive improvements to EffectorP, the first machine learning classifier for fungal effector prediction. EffectorP 2.0 is now trained on a larger set of effectors and utilizes a different approach based on an ensemble of classifiers trained on different subsets of negative data, offering different views on classification. EffectorP 2.0 achieves an accuracy of 89%, compared with 82% for EffectorP 1.0 and 59.8% for a small size classifier. Important features for effector prediction appear to be protein size, protein net charge as well as the amino acids serine and cysteine. EffectorP 2.0 decreases the number of predicted effectors in secretomes of fungal plant symbionts and saprophytes by 40% when compared with EffectorP 1.0. However, EffectorP 1.0 retains value, and combining EffectorP 1.0 and 2.0 results in a stringent classifier with a low false positive rate of 9%. EffectorP 2.0 predicts significant enrichments of effectors in 12 of 13 sets of infection-induced proteins from diverse fungal pathogens, whereas a small cysteine-rich classifier detects enrichment in only seven of 13. EffectorP 2.0 will fast track the prioritization of high-confidence effector candidates for functional validation and aid in improving our understanding of effector biology. EffectorP 2.0 is available at http://effectorp.csiro.au.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
| | - Peter N. Dodds
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and FoodQueensland Bioscience PrecinctBrisbane, Qld 4067Australia
| | - Karam B. Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
- Department of Environment and Agriculture, Centre for Crop and Disease ManagementCurtin UniversityBentley, WA 6102Australia
| | - Jennifer M. Taylor
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
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22
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Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Cut-and-Paste Transposons in Fungi with Diverse Lifestyles. Genome Biol Evol 2017; 9:3463-3477. [PMID: 29228286 PMCID: PMC5751038 DOI: 10.1093/gbe/evx261] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 02/06/2023] Open
Abstract
Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut-and-paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species' lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition.
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Affiliation(s)
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland
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23
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Sessegolo C, Burlet N, Haudry A. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biol Lett 2017; 12:rsbl.2016.0407. [PMID: 27576524 PMCID: PMC5014035 DOI: 10.1098/rsbl.2016.0407] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/08/2016] [Indexed: 01/28/2023] Open
Abstract
While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup.
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Affiliation(s)
- Camille Sessegolo
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, 69100 Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, 69100 Villeurbanne, France
| | - Annabelle Haudry
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, 69100 Villeurbanne, France
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24
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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] [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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25
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Clutterbuck AJ. Genomic CG dinucleotide deficiencies associated with transposable element hypermutation in Basidiomycetes, some lower fungi, a moss and a clubmoss. Fungal Genet Biol 2017; 104:16-28. [PMID: 28438577 DOI: 10.1016/j.fgb.2017.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/10/2017] [Accepted: 04/17/2017] [Indexed: 12/15/2022]
Abstract
Many Basidiomycete genomes include substantial fractions that are deficient in CG dinucleotides, in extreme cases amounting to 70% of the genome. CG deficiency is variable and correlates with genome size and, more closely, with transposable element (TE) content. Many species have limited CG deficiency; it is therefore likely that there are other mechanisms that can control TE proliferation. Examination of TEs confirms that C-to-T transition mutations in CG dinucleotides may comprise a conspicuous proportion of differences between paired elements, however transition/transversion ratios are never as high as those due to RIP in some Ascomycetes, suggesting that repeat-associated CG mutation is not totally pervasive. This has allowed gene family expansion in Basidiomycetes, although CG transition differences are often prominent in paired gene family members, and are evidently responsible for destruction of some copies. A few lower fungal genomes exhibit similar evidence of repeat-associated CG mutation, as do the genomes of the two lower plants Physcomitrella patens and Selaginella moellendorffii, in both of which mutation parallels published methylation of CHG as well as CG nucleotides. In Basidiomycete DNA methylation has been reported to be largely confined to CG dinucleotides in repetitive DNA, but while methylation and mutation are evidently associated, it is not clear which is cause and which effect.
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Affiliation(s)
- A John Clutterbuck
- Wolfson Link Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
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26
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Castanera R, Borgognone A, Pisabarro AG, Ramírez L. Biology, dynamics, and applications of transposable elements in basidiomycete fungi. Appl Microbiol Biotechnol 2017; 101:1337-1350. [PMID: 28074220 DOI: 10.1007/s00253-017-8097-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/20/2016] [Accepted: 01/02/2017] [Indexed: 11/25/2022]
Abstract
The phylum Basidiomycota includes filamentous fungi and yeast species with different ecological and genomic characteristics. Transposable elements (TEs) are abundant components of most eukaryotic genomes, and their transition from being genomic parasites to key drivers of genomic architecture, functionality, and evolution is a subject receiving much attention. In light of the abundant genomic information released during the last decade, the aims of this mini-review are to discuss the dynamics and impact of TEs in basidiomycete fungi. To do this, we surveyed and explored data from 75 genomes, which encompass the phylogenetic diversity of the phylum Basidiomycota. We describe annotation approaches and analyze TE distribution in the context of species phylogeny and genome size. Further, we review the most relevant literature about the role of TEs in species lifestyle, their impact on genome architecture and functionality, and the defense mechanisms evolved to control their proliferation. Finally, we discuss potential applications of TEs that can drive future innovations in fungal research.
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Affiliation(s)
- Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Alessandra Borgognone
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain.
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27
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Szitenberg A, Cha S, Opperman CH, Bird DM, Blaxter ML, Lunt DH. Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements. Genome Biol Evol 2016; 8:2964-2978. [PMID: 27566762 PMCID: PMC5635653 DOI: 10.1093/gbe/evw208] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2016] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host's genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.
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Affiliation(s)
- Amir Szitenberg
- Evolutionary Biology Group, School of Environmental Sciences, University of Hull, England, United Kingdom The Dead Sea and Arava Science Center, Israel
| | - Soyeon Cha
- Department of Plant Pathology, North Carolina State University
| | | | - David M Bird
- Department of Plant Pathology, North Carolina State University
| | - Mark L Blaxter
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Scotland
| | - David H Lunt
- Evolutionary Biology Group, School of Environmental Sciences, University of Hull, England, United Kingdom
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29
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Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, Grimwood J, Pérez G, Pisabarro AG, Grigoriev IV, Stajich JE, Ramírez L. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLoS Genet 2016; 12:e1006108. [PMID: 27294409 PMCID: PMC4905642 DOI: 10.1371/journal.pgen.1006108] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 05/13/2016] [Indexed: 11/17/2022] Open
Abstract
Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation. Transposable elements (TEs) are enigmatic genetic units that have played important roles in the evolution of eukaryotic genomes. Since their discovery in the 1950s, they have gained increasing attention and are known today as active genome modelers in multiple species. Although these elements have been widely studied in plants, much less is known about their occurrence and impact on the fungal kingdom. Using a diverse set of basidiomycete and ascomycete fungi, we quantified and characterized a huge diversity of DNA and RNA transposable elements, and we identified species that had 0.02 to 29.8% of their genomes occupied by transposable elements. In addition, using our basidiomycete model Pleurotus ostreatus, we demonstrated how TE insertions produced detrimental effects on the expression of upstream and downstream genes, which were downregulated compared with the control groups. This silencing mechanism was present in the basidiomycetes tested but exhibited a patchy distribution in ascomycetes, and might be related to specific genome defense mechanisms that control transposon proliferation. This finding reveals the broader impact of transposable elements in fungi. In addition to their importance as long-term evolutionary forces, they play major roles in the more dynamic transcriptome regulation of certain species.
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Affiliation(s)
- Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Leticia López-Varas
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Alessandra Borgognone
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alla Lapidus
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.,Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.,Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Jane Grimwood
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.,Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Gúmer Pérez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jason E Stajich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, United States of America
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
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30
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Alfaro M, Castanera R, Lavín JL, Grigoriev IV, Oguiza JA, Ramírez L, Pisabarro AG. Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungusPleurotus ostreatus. Environ Microbiol 2016; 18:4710-4726. [DOI: 10.1111/1462-2920.13360] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Alfaro
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - Raúl Castanera
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - José L. Lavín
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
- Genome Analysis Platform, CIC bioGUNE & CIBERehd, Bizkaia Technology Park; Derio 48160 Spain
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute; Walnut Creek CA 94598 USA
| | - José A. Oguiza
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - Lucía Ramírez
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
| | - Antonio G. Pisabarro
- Department of Agrarian Production; Genetics and Microbiology Research Group, Public University of Navarre; Pamplona 31006 Spain
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31
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Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, Amirebrahimi M, Hesse CN, Spatafora JW, Henrissat B, Hainaut M, Grigoriev IV, Hibbett DS. The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol 2015; 120:26-42. [PMID: 26693682 DOI: 10.1016/j.funbio.2015.10.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Xylona heveae has only been isolated as an endophyte of rubber trees. In an effort to understand the genetic basis of endophytism, we compared the genome contents of X. heveae and 36 other Ascomycota with diverse lifestyles and nutritional modes. We focused on genes that are known to be important in the host-fungus interaction interface and that presumably have a role in determining the lifestyle of a fungus. We used phylogenomic data to infer the higher-level phylogenetic position of the Xylonomycetes, and mined ITS sequences to explore its taxonomic and ecological diversity. The X. heveae genome contains a low number of enzymes needed for plant cell wall degradation, suggesting that Xylona is a highly adapted specialist and likely dependent on its host for survival. The reduced repertoire of carbohydrate active enzymes could reflect an adaptation to intercellulary growth and to the avoidance of the host's immune system, suggesting that Xylona has a strictly endophytic lifestyle. Phylogenomic data resolved the position of Xylonomycetes as sister to Lecanoromycetes and Eurotiomycetes and placed the beetle-endosymbiont Symbiotaphrina as a member of this class. ITS data revealed that Trinosporium is also part of the Xylonomycetes, extending the taxonomic and ecological diversity of this group.
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Affiliation(s)
- Romina Gazis
- Clark University, Biology Department, 950 Main Street, Worcester, MA 01610, USA.
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Junyan Lin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Cedar N Hesse
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, USA; Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Joseph W Spatafora
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, USA
| | - Bernard Henrissat
- Aix-Marseille Université, CNRS, UMR 7257, Marseille, France; Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille cedex 9, France; King Abdulaziz University, Department of Biological Sciences, Jeddah 21589, Saudi Arabia
| | | | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - David S Hibbett
- Clark University, Biology Department, 950 Main Street, Worcester, MA 01610, USA
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32
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Wagner K, Linde J, Krause K, Gube M, Koestler T, Sammer D, Kniemeyer O, Kothe E. Tricholoma vaccinum host communication during ectomycorrhiza formation. FEMS Microbiol Ecol 2015; 91:fiv120. [PMID: 26449385 DOI: 10.1093/femsec/fiv120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2015] [Indexed: 11/14/2022] Open
Abstract
The genome sequence of Tricholoma vaccinum was obtained to predict its secretome in order to elucidate communication of T. vaccinum with its host tree spruce (Picea abies) in interkingdom signaling. The most prominent protein domains within the 206 predicted secreted proteins belong to energy and nutrition (52%), cell wall degradation (19%) and mycorrhiza establishment (9%). Additionally, we found small secreted proteins that show typical features of effectors potentially involved in host communication. From the secretome, 22 proteins could be identified, two of which showed higher protein abundances after spruce root exudate exposure, while five were downregulated in this treatment. The changes in T. vaccinum protein excretion with first recognition of the partner were used to identify small secreted proteins with the potential to act as effectors in the mutually beneficial symbiosis. Our observations support the hypothesis of a complex communication network including a cocktail of communication molecules induced long before physical contact of the partners.
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Affiliation(s)
- Katharina Wagner
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07745 Jena, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Beutenbergstraße 11a, 07745 Jena, Germany
| | - Katrin Krause
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07745 Jena, Germany
| | - Matthias Gube
- Soil Science of Temperate Ecosystems, Georg August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Tina Koestler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, A-1030 Vienna, Austria
| | - Dominik Sammer
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07745 Jena, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Beutenbergstraße 11a, 07745 Jena, Germany
| | - Erika Kothe
- Institute of Microbiology, Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07745 Jena, Germany
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33
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Dentinger BTM, Gaya E, O'Brien H, Suz LM, Lachlan R, Díaz-Valderrama JR, Koch RA, Aime MC. Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12553] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Bryn T. M. Dentinger
- Jodrell Laboratory; Royal Botanic Gardens; Kew TW9 3DS UK
- Institute of Biological, Environmental and Rural Sciences; Aberystwyth University; Cledwyn Building Penglais Aberystwyth SY23 3DD UK
| | - Ester Gaya
- Jodrell Laboratory; Royal Botanic Gardens; Kew TW9 3DS UK
| | - Heath O'Brien
- School of Biological Sciences; University of Bristol; Life Sciences Building 24 Tyndall Avenue Bristol BS8 1TQ UK
| | - Laura M. Suz
- Jodrell Laboratory; Royal Botanic Gardens; Kew TW9 3DS UK
| | - Robert Lachlan
- Department of Psychology; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Jorge R. Díaz-Valderrama
- Department of Botany and Plant Pathology; Purdue University; 915 W. State St. West Lafayette IN 47907 USA
| | - Rachel A. Koch
- Department of Botany and Plant Pathology; Purdue University; 915 W. State St. West Lafayette IN 47907 USA
| | - M. Catherine Aime
- Department of Botany and Plant Pathology; Purdue University; 915 W. State St. West Lafayette IN 47907 USA
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Chaib De Mares M, Hess J, Floudas D, Lipzen A, Choi C, Kennedy M, Grigoriev IV, Pringle A. Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita. THE NEW PHYTOLOGIST 2015; 205:1552-1564. [PMID: 25407899 DOI: 10.1111/nph.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/24/2014] [Indexed: 06/04/2023]
Abstract
The genus Amanita encompasses both symbiotic, ectomycorrhizal fungi and asymbiotic litter decomposers; all species are derived from asymbiotic ancestors. Symbiotic species are no longer able to degrade plant cell walls. The carbohydrate esterases family 1 (CE1s) is a diverse group of enzymes involved in carbon metabolism, including decomposition and carbon storage. CE1 genes of the ectomycorrhizal A. muscaria appear diverged from all other fungal homologues, and more similar to CE1s of bacteria, suggesting a horizontal gene transfer (HGT) event. In order to test whether AmanitaCE1s were acquired horizontally, we built a phylogeny of CE1s collected from across the tree of life, and describe the evolution of CE1 genes among Amanita and relevant lineages of bacteria. CE1s of symbiotic Amanita were very different from CE1s of asymbiotic Amanita, and are more similar to bacterial CE1s. The protein structure of one CE1 gene of A. muscaria matched a depolymerase that degrades the carbon storage molecule poly((R)-3-hydroxybutyrate) (PHB). Asymbiotic Amanita do not carry sequence or structural homologues of these genes. The CE1s acquired through HGT may enable novel metabolisms, or play roles in signaling or defense. This is the first evidence for the horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal fungi.
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Affiliation(s)
- Maryam Chaib De Mares
- Department of Microbial Ecology, University of Groningen, 9747 AG, Groningen, the Netherlands
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jaqueline Hess
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biosciences, University of Oslo, 0371, Oslo, Norway
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Megan Kennedy
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anne Pringle
- Harvard Forest, 324 North Main Street, Petersham, MA, 01366, USA
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Floudas D, Held BW, Riley R, Nagy LG, Koehler G, Ransdell AS, Younus H, Chow J, Chiniquy J, Lipzen A, Tritt A, Sun H, Haridas S, LaButti K, Ohm RA, Kües U, Blanchette RA, Grigoriev IV, Minto RE, Hibbett DS. Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genet Biol 2015; 76:78-92. [PMID: 25683379 DOI: 10.1016/j.fgb.2015.02.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/26/2014] [Accepted: 02/05/2015] [Indexed: 11/17/2022]
Abstract
Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C. torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C. torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited.
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Affiliation(s)
- Dimitrios Floudas
- Department of Biology, Clark University, 950 Main St, Worcester 01610, MA, USA; MEMEG, Ecology Building Sölvegatan 37, 223 62, Lund, Sweden.
| | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108-6030, USA.
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Laszlo G Nagy
- Department of Biology, Clark University, 950 Main St, Worcester 01610, MA, USA; Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Gage Koehler
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - Anthony S Ransdell
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - Hina Younus
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - Julianna Chow
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Jennifer Chiniquy
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Hui Sun
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Sajeet Haridas
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Robin A Ohm
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA; Microbiology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Ursula Kües
- Institute for Forest Botany, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108-6030, USA.
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA.
| | - Robert E Minto
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, LD326, 402 N Blackford St, Indianapolis, IN 46202, USA.
| | - David S Hibbett
- Department of Biology, Clark University, 950 Main St, Worcester 01610, MA, USA.
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van der Nest MA, Beirn LA, Crouch JA, Demers JE, de Beer ZW, De Vos L, Gordon TR, Moncalvo JM, Naidoo K, Sanchez-Ramirez S, Roodt D, Santana QC, Slinski SL, Stata M, Taerum SJ, Wilken PM, Wilson AM, Wingfield MJ, Wingfield BD. IMA Genome-F 3: Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila. IMA Fungus 2014; 5:473-86. [PMID: 25734036 PMCID: PMC4329328 DOI: 10.5598/imafungus.2014.05.02.11] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 12/04/2014] [Indexed: 12/24/2022] Open
Abstract
The genomes of fungi provide an important resource to resolve issues pertaining to their taxonomy, biology, and evolution. The genomes of Amanita jacksonii, Ceratocystis albifundus, a Fusarium circinatum variant, Huntiella omanensis, Leptographium procerum, Sclerotinia echinophila, and Rutstroemia sydowiana are presented in this genome announcement. These seven genomes are from a number of fungal pathogens and economically important species. The genome sizes range from 27 Mb in the case of Ceratocystis albifundus to 51.9 Mb for Rutstroemia sydowiana. The latter also encodes for a predicted 17 350 genes, more than double that of Ceratocystis albifundus. These genomes will add to the growing body of knowledge of these fungi and provide a value resource to researchers studying these fungi.
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Affiliation(s)
- Magriet A van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Lisa A Beirn
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Jo Anne Crouch
- Systematic Mycology and Microbiology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Jill E Demers
- Systematic Mycology and Microbiology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Thomas R Gordon
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Jean-Marc Moncalvo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada ; Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada ; Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Santiago Sanchez-Ramirez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Danielle Roodt
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Quentin C Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Stephanie L Slinski
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa; ; Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen J Taerum
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - P Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Andrea M Wilson
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
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