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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Kollár J, Poulíčková A, Dvořák P. On the relativity of species, or the probabilistic solution to the species problem. Mol Ecol 2021; 31:411-418. [PMID: 34626519 DOI: 10.1111/mec.16218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 09/17/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Abstract
For centuries, both scientists and philosophers have discussed the nature of species resulting in c. 35 species concepts proposed to date. However, in our opinion, none of them incorporated neither recent advances in evolutionary genomics nor dimensionality of species in befitting depth. Our attempt to do so resulted in the following conclusions. Due to the continuous nature of evolution (regardless of its rate and constancy), species are inevitably undefinable as natural discontinuous units (except those originating in saltatory speciation) whenever the time dimension is taken into consideration. Therefore, the very existence of species as a natural discontinuous entity is relative to its dimensionality. A direct consequence of the relativity of species is the duality of speciators (e.g., incipient species) meaning that, in a given time, they may be perceived as both being and not being a species. Finally, the most accurate way to reflect both the relativity of species and the duality of speciators in species delimitation is probabilistic. While the novelty of these ideas may be questionable, they still deserve more extensive attention from the biological community. Here, we hope to draw such attention by outlining one of the possible pathways towards a new kind of probabilistic species delimitation methods based on the probability of irreversible divergence of evolutionary lineages. We anticipate that our probabilistic view of speciation has the potential to facilitate some of the most serious and universal issues of current taxonomy and to ensure unity of the species-level taxonomy across the tree of life.
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Affiliation(s)
- Jan Kollár
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Aloisie Poulíčková
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
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Zhang J, Shen N, Li C, Xiang X, Liu G, Gui Y, Patev S, Hibbett DS, Barry K, Andreopoulos W, Lipzen A, Riley R, He G, Yan M, Grigoriev IV, Shan Kwan H, Kit Cheung M, Bian Y, Xiao Y. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes. J Adv Res 2021; 38:91-106. [PMID: 35572413 PMCID: PMC9091725 DOI: 10.1016/j.jare.2021.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 02/08/2023] Open
Abstract
We detected three subgroups of L. edodes with robust phenotypic differentiation. The three subgroups were diverged 36,871 generations ago. L. edodes cultivars in China might originate from the vicinity of Northeast China. We dissected the genetic basis of adaptive evolution in L. edodes. Genes related to fruiting body development are involved in adaptive evolution.
Introduction Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
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The Predicted Mannosyltransferase GT69-2 Antagonizes RFW-1 To Regulate Cell Fusion in Neurospora crassa. mBio 2021; 12:mBio.00307-21. [PMID: 33727349 PMCID: PMC8092235 DOI: 10.1128/mbio.00307-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Filamentous fungi undergo somatic cell fusion to create a syncytial, interconnected hyphal network which confers a fitness benefit during colony establishment. However, barriers to somatic cell fusion between genetically different cells have evolved that reduce invasion by parasites or exploitation by maladapted genetic entities (cheaters). Here, we identified a predicted mannosyltransferase, glycosyltransferase family 69 protein (GT69-2) that was required for somatic cell fusion in Neurospora crassa Cells lacking GT69-2 prematurely ceased chemotropic signaling and failed to complete cell wall dissolution and membrane merger in pairings with wild-type cells or between Δgt69-2 cells (self fusion). However, loss-of-function mutations in the linked regulator of cell fusion and cell wall remodeling-1 (rfw-1) locus suppressed the self-cell-fusion defects of Δgt69-2 cells, although Δgt69-2 Δrfw-1 double mutants still failed to undergo fusion with wild-type cells. Both GT69-2 and RFW-1 localized to the Golgi apparatus. Genetic analyses indicated that RFW-1 negatively regulates cell wall remodeling-dependent processes, including cell wall dissolution during cell fusion, separation of conidia during asexual sporulation, and conidial germination. GT69-2 acts as an antagonizer to relieve or prevent negative functions on cell fusion by RFW-1. In Neurospora species and N. crassa populations, alleles of gt69-2 were highly polymorphic and fell into two discrete haplogroups. In all isolates within haplogroup I, rfw-1 was conserved and linked to gt69-2 All isolates within haplogroup II lacked rfw-1. These data indicated that gt69-2/rfw-1 are under balancing selection and provide new mechanisms regulating cell wall remodeling during cell fusion and conidial separation.IMPORTANCE Cell wall remodeling is a dynamic process that balances cell wall integrity versus cell wall dissolution. In filamentous fungi, cell wall dissolution is required for somatic cell fusion and conidial separation during asexual sporulation. In the filamentous fungus Neurospora crassa, allorecognition checkpoints regulate the cell fusion process between genetically different cells. Our study revealed two linked loci with transspecies polymorphisms and under coevolution, rfw-1 and gt69-2, which form a coordinated system to regulate cell wall remodeling during somatic cell fusion, conidial separation, and asexual spore germination. RFW-1 acts as a negative regulator of these three processes, while GT69-2 functions antagonistically to RFW-1. Our findings provide new insight into the mechanisms involved in regulation of fungal cell wall remodeling during growth and development.
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Gladieux P, De Bellis F, Hann-Soden C, Svedberg J, Johannesson H, Taylor JW. Neurospora from Natural Populations: Population Genomics Insights into the Life History of a Model Microbial Eukaryote. Methods Mol Biol 2021; 2090:313-336. [PMID: 31975173 DOI: 10.1007/978-1-0716-0199-0_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Fabien De Bellis
- UMR AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Christopher Hann-Soden
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jesper Svedberg
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
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Gene Copy Number Variation Does Not Reflect Structure or Environmental Selection in Two Recently Diverged California Populations of Suillus brevipes. G3 (BETHESDA, MD.) 2020; 10:4591-4597. [PMID: 33051263 PMCID: PMC7718732 DOI: 10.1534/g3.120.401735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene copy number variation across individuals has been shown to track population structure and be a source of adaptive genetic variation with significant fitness impacts. In this study, we report opposite results for both predictions based on the analysis of gene copy number variants (CNVs) of Suillus brevipes, a mycorrhizal fungus adapted to coastal and montane habitats in California. In order to assess whether gene copy number variation mirrored population structure and selection in this species, we investigated two previously studied locally adapted populations showing a highly differentiated genomic region encompassing a gene predicted to confer salt tolerance. In addition, we examined whether copy number in the genes related to salt homeostasis was differentiated between the two populations. Although we found many instances of CNV regions across the genomes of S. brevipes individuals, we also found CNVs did not recover population structure and known salt-tolerance-related genes were not under selection across the coastal population. Our results contrast with predictions of CNVs matching single-nucleotide polymorphism divergence and showed CNVs of genes for salt homeostasis are not under selection in S. brevipes.
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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Nespolo RF, Villarroel CA, Oporto CI, Tapia SM, Vega-Macaya F, Urbina K, De Chiara M, Mozzachiodi S, Mikhalev E, Thompson D, Larrondo LF, Saenz-Agudelo P, Liti G, Cubillos FA. An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages. PLoS Genet 2020; 16:e1008777. [PMID: 32357148 PMCID: PMC7219788 DOI: 10.1371/journal.pgen.1008777] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/13/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
Population‐level sampling and whole‐genome sequences of different individuals allow one to identify signatures of hybridization, gene flow and potential molecular mechanisms of environmental responses. Here, we report the isolation of 160 Saccharomyces eubayanus strains, the cryotolerant ancestor of lager yeast, from ten sampling sites in Patagonia along 2,000 km of Nothofagus forests. Frequency of S. eubayanus isolates was higher towards southern and colder regions, demonstrating the cryotolerant nature of the species. We sequenced the genome of 82 strains and, together with 23 available genomes, performed a comprehensive phylogenetic analysis. Our results revealed the presence of five different lineages together with dozens of admixed strains. Various analytical methods reveal evidence of gene flow and historical admixture between lineages from Patagonia and Holarctic regions, suggesting the co-occurrence of these ancestral populations. Analysis of the genetic contribution to the admixed genomes revealed a Patagonian genetic origin of the admixed strains, even for those located in the North Hemisphere. Overall, the Patagonian lineages, particularly the southern populations, showed a greater global genetic diversity compared to Holarctic and Chinese lineages, in agreement with a higher abundance in Patagonia. Thus, our results are consistent with a likely colonization of the species from peripheral glacial refugia from South Patagonia. Furthermore, fermentative capacity and maltose consumption resulted negatively correlated with latitude, indicating better fermentative performance in northern populations. Our genome analysis, together with previous reports in the sister species S. uvarum suggests that a S. eubayanus ancestor was adapted to the harsh environmental conditions of Patagonia, a region that provides the ecological conditions for the diversification of these ancestral lineages. Lager yeast history has intrigued scientists for decades. The recent isolation of S. eubayanus, the lager yeast ancestor, represents an unprecedented opportunity to extend our knowledge on yeast phylogeography and the origins of the S. pastorianus lager hybrid. However, the genetic, phenotypic and evolutionary history of this species remains poorly known. Our work demonstrates that S. eubayanus isolates from Patagonia have the greatest genetic diversity, comprising the largest number of lineages within a single geographic region and experienced ancestral and recent admixture between lineages, likely suggesting co-occurrence in Patagonia. Importantly, some isolates exhibited significant phenotypic differences for traits such as high temperature and ethanol tolerance, together with fermentation performance, demonstrating their potential in the brewing industry for the generation of new styles of lager beers. Furthermore, our results support the idea of colonization from peripheral glacial refugia from the South, as responsible for the high genetic diversity observed in southern Chilean Patagonia. Our results allow hypothesizing a successful physiological adjustment of the species to the local conditions in Patagonia, explaining its wide distribution in the southern hemisphere.
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Affiliation(s)
- Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Carlos A. Villarroel
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Christian I. Oporto
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | | | - Franco Vega-Macaya
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Kamila Urbina
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | | | | | | | - Dawn Thompson
- Ginkgo Bioworks, Boston, Massachusetts, United States of America
| | - Luis F. Larrondo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Gianni Liti
- Université Côte d’Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Francisco A. Cubillos
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
- * E-mail:
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Daskalov A, Gladieux P, Heller J, Glass NL. Programmed Cell Death in Neurospora crassa Is Controlled by the Allorecognition Determinant rcd-1. Genetics 2019; 213:1387-1400. [PMID: 31636083 PMCID: PMC6893366 DOI: 10.1534/genetics.119.302617] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 10/17/2019] [Indexed: 12/31/2022] Open
Abstract
Nonself recognition following cell fusion between genetically distinct individuals of the same species in filamentous fungi often results in a programmed cell death (PCD) reaction, where the heterokaryotic fusion cell is compartmentalized and rapidly killed. The allorecognition process plays a key role as a defense mechanism that restricts genome exploitation, resource plundering, and the spread of deleterious senescence plasmids and mycoviruses. Although a number of incompatibility systems have been described that function in mature hyphae, less is known about the PCD pathways in asexual spores, which represent the main infectious unit in various human and plant fungal pathogens. Here, we report the identification of regulator of cell death-1 (rcd-1), a novel allorecognition gene, controlling PCD in germinating asexual spores of Neurospora crassa; rcd-1 is one of the most polymorphic genes in the genomes of wild N. crassa isolates. The coexpression of two antagonistic rcd-1-1 and rcd-1-2 alleles was necessary and sufficient to trigger cell death in fused germlings and in hyphae. Based on analysis of wild populations of N. crassa and N. discreta, rcd-1 alleles appeared to be under balancing selection and associated with trans-species polymorphisms. We shed light on genomic rearrangements that could have led to the emergence of the incompatibility system in Neurospora and show that rcd-1 belongs to a much larger gene family in fungi. Overall, our work contributes toward a better understanding of allorecognition and PCD in an underexplored developmental stage of filamentous fungi.
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Affiliation(s)
- Asen Daskalov
- Plant and Microbial Biology Department, The University of California, Berkeley, California 94720
| | - Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier SupAgro, University Montpellier, 34060, France
| | - Jens Heller
- Plant and Microbial Biology Department, The University of California, Berkeley, California 94720
- Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, California 94720
| | - N Louise Glass
- Plant and Microbial Biology Department, The University of California, Berkeley, California 94720
- Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, California 94720
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11
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Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe. Fungal Genet Biol 2019; 130:122-133. [DOI: 10.1016/j.fgb.2019.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023]
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12
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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Galtier N. Delineating species in the speciation continuum: A proposal. Evol Appl 2019; 12:657-663. [PMID: 30976300 PMCID: PMC6439491 DOI: 10.1111/eva.12748] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/08/2018] [Indexed: 12/18/2022] Open
Abstract
Delineating species is a difficult and seemingly uninteresting issue that is still essential to address. Taxonomic methodology is heterogeneous according to the taxa and scientists involved due to the disparate data quality and quantity and disagreements over the species concept. This has negative impacts on basic and applied research. Genomic data substantially enhance our understanding of the speciation process but do not provide a ubiquitous solution to the species problem. The relevance of comparative approaches in speciation research has nevertheless recently been demonstrated. I suggest moving towards a more unified taxonomic classification through a reference-based decision procedure.
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Affiliation(s)
- Nicolas Galtier
- UMR 5554 – Institut des Sciences de l'EvolutionCNRS – University of Montpellier – IRD – EPHEMontpellierFrance
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14
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Phylogenomics, biogeography, and adaptive radiation of grapes. Mol Phylogenet Evol 2018; 129:258-267. [DOI: 10.1016/j.ympev.2018.08.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/27/2022]
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15
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Atanasova L, Dubey M, Grujić M, Gudmundsson M, Lorenz C, Sandgren M, Kubicek CP, Jensen DF, Karlsson M. Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family. BMC Microbiol 2018; 18:178. [PMID: 30404596 PMCID: PMC6223089 DOI: 10.1186/s12866-018-1310-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 10/10/2018] [Indexed: 11/29/2022] Open
Abstract
Background Pectin is one of the major and most complex plant cell wall components that needs to be overcome by microorganisms as part of their strategies for plant invasion or nutrition. Microbial pectinolytic enzymes therefore play a significant role for plant-associated microorganisms and for the decomposition and recycling of plant organic matter. Recently, comparative studies revealed significant gene copy number expansion of the polysaccharide lyase 1 (PL1) pectin/pectate lyase gene family in the Clonostachys rosea genome, while only low numbers were found in Trichoderma species. Both of these fungal genera are widely known for their ability to parasitize and kill other fungi (mycoparasitism) and certain species are thus used for biocontrol of plant pathogenic fungi. Results In order to understand the role of the high number of pectin degrading enzymes in Clonostachys, we studied diversity and evolution of the PL1 gene family in C. rosea compared with other Sordariomycetes with varying nutritional life styles. Out of 17 members of C. rosea PL1, we could only detect two to be secreted at acidic pH. One of them, the pectate lyase pel12 gene was found to be strongly induced by pectin and, to a lower degree, by polygalacturonic acid. Heterologous expression of the PEL12 in a PL1-free background of T. reesei revealed direct enzymatic involvement of this protein in utilization of pectin at pH 5 without a requirement for Ca2+. The mutants showed increased utilization of pectin compounds, but did not increase biocontrol ability in detached leaf assay against the plant pathogen Botrytis cinerea compared to the wild type. Conclusions In this study, we aimed to gain insight into diversity and evolution of the PL1 gene family in C. rosea and other Sordariomycete species in relation to their nutritional modes. We show that C. rosea PL1 expansion does not correlate with its mycoparasitic nutritional mode and resembles those of strong plant pathogenic fungi. We further investigated regulation, specificity and function of the C. rosea PEL12 and show that this enzyme is directly involved in degradation of pectin and pectin-related compounds, but not in C. rosea biocontrol. Electronic supplementary material The online version of this article (10.1186/s12866-018-1310-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lea Atanasova
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden. .,Research division of Biochemical Technology, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, 1060, Vienna, Austria. .,Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria.
| | - Mukesh Dubey
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden
| | - Marica Grujić
- Research division of Biochemical Technology, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, 1060, Vienna, Austria
| | - Mikael Gudmundsson
- Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-75007, Uppsala, Sweden
| | - Cindy Lorenz
- Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Mats Sandgren
- Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-75007, Uppsala, Sweden
| | - Christian P Kubicek
- Research division of Biochemical Technology, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, 1060, Vienna, Austria.,, Present address: Steinschötelgasse 7, 1100, Vienna, Austria
| | - Dan Funck Jensen
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden
| | - Magnus Karlsson
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden
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16
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Vieira A, Silva DN, Várzea V, Paulo OS, Batista D. Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica. MOLECULAR PLANT PATHOLOGY 2018; 19:2488-2501. [PMID: 30073748 PMCID: PMC6638157 DOI: 10.1111/mpp.12726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/25/2018] [Accepted: 06/28/2018] [Indexed: 05/19/2023]
Abstract
Pathogenic fungi are emerging at an increasing rate on a wide range of host plants, leading to tremendous threats to the global economy and food safety. Several plant pathogens have been considered to be invasive species, rendering large-scale population genomic analyses crucial to better understand their demographic history and evolutionary potential. Colletotrichum kahawae (Ck) is a highly aggressive and specialized pathogen, causing coffee berry disease in Arabica coffee in Africa. This pathogen leads to severe production losses and its dissemination out of Africa is greatly feared. To address this issue, a population genomic approach using thousands of single nucleotide polymorphisms (SNPs) spaced throughout the genome was used to unveil its demographic history and evolutionary potential. The current study confirms that Ck is a true clonal pathogen, perfectly adapted to green coffee berries, with three completely differentiated populations (Angolan, Cameroonian and East African). Two independent clonal lineages were found within the Angolan population as opposed to the remaining single clonal populations. The most probable colonization scenario suggests that this pathogen emerged in Angola and immediately dispersed to East Africa, where these two populations began to differentiate, followed by the introduction in Cameroon from an Angolan population. However, the differentiation between the two Angolan clonal lineages masks the mechanism for the emergence of the Cameroonian population. Our results suggest that Ck is completely differentiated from the ancestral lineage, has a low evolutionary potential and a low dispersion ability, with human transport the most likely scenario for its potential dispersion, which makes the fulfilment of the quarantine measures and management practices implemented crucial.
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Affiliation(s)
- Ana Vieira
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
| | - Diogo Nuno Silva
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
| | - Victor Várzea
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
| | - Octávio Salgueiro Paulo
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
| | - Dora Batista
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
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17
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18
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Allison SD, Romero-Olivares AL, Lu Y, Taylor JW, Treseder KK. Temperature sensitivities of extracellular enzyme V max and K m across thermal environments. GLOBAL CHANGE BIOLOGY 2018; 24:2884-2897. [PMID: 29322601 DOI: 10.1111/gcb.14045] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/14/2017] [Accepted: 12/20/2017] [Indexed: 05/12/2023]
Abstract
The magnitude and direction of carbon cycle feedbacks under climate warming remain uncertain due to insufficient knowledge about the temperature sensitivities of soil microbial processes. Enzymatic rates could increase at higher temperatures, but this response could change over time if soil microbes adapt to warming. We used the Arrhenius relationship, biochemical transition state theory, and thermal physiology theory to predict the responses of extracellular enzyme Vmax and Km to temperature. Based on these concepts, we hypothesized that Vmax and Km would correlate positively with each other and show positive temperature sensitivities. For enzymes from warmer environments, we expected to find lower Vmax , Km , and Km temperature sensitivity but higher Vmax temperature sensitivity. We tested these hypotheses with isolates of the filamentous fungus Neurospora discreta collected from around the globe and with decomposing leaf litter from a warming experiment in Alaskan boreal forest. For Neurospora extracellular enzymes, Vmax Q10 ranged from 1.48 to 2.25, and Km Q10 ranged from 0.71 to 2.80. In agreement with theory, Vmax and Km were positively correlated for some enzymes, and Vmax declined under experimental warming in Alaskan litter. However, the temperature sensitivities of Vmax and Km did not vary as expected with warming. We also found no relationship between temperature sensitivity of Vmax or Km and mean annual temperature of the isolation site for Neurospora strains. Declining Vmax in the Alaskan warming treatment implies a short-term negative feedback to climate change, but the Neurospora results suggest that climate-driven changes in plant inputs and soil properties are important controls on enzyme kinetics in the long term. Our empirical data on enzyme Vmax , Km , and temperature sensitivities should be useful for parameterizing existing biogeochemical models, but they reveal a need to develop new theory on thermal adaptation mechanisms.
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Affiliation(s)
- Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | | | - Ying Lu
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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19
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Maxwell CS, Sepulveda VE, Turissini DA, Goldman WE, Matute DR. Recent admixture between species of the fungal pathogen Histoplasma. Evol Lett 2018; 2:210-220. [PMID: 30283677 PMCID: PMC6121842 DOI: 10.1002/evl3.59] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 12/30/2022] Open
Abstract
Hybridization between species of pathogens has the potential to speed evolution of virulence by providing the raw material for adaptation through introgression or by assembling new combinations of virulence traits. Fungal diseases are a source high morbidity, and remain difficult to treat. Yet the frequency of hybridization between fungal species has rarely been explored, and the functional role of introgressed alleles remains largely unknown. Histoplasma mississippiense and H. ohiense are sympatric throughout their range in North America and have distinct virulence strategies, making them an ideal system to examine the role introgression may play in fungal pathogens. We identified introgressed tracts in the genomes of a sample of H. mississippiense and H. ohiense isolates. We found strong evidence in each species for recent admixture, but introgressed alleles were present at low frequencies, suggesting that they were deleterious. Consistent with this, coding and regulatory sequences were strongly depleted within introgressed regions, whereas intergenic regions were enriched, indicating that functional introgressed alleles were frequently deleterious in their new genomic context. Surprisingly, we found only two isolates with substantial admixture: the H. mississippiense and H. ohiense genomic reference strains, WU24 and G217B, respectively. Our results show that recent admixture has occurred, that it is frequently deleterious and that conclusions based on studies of the H. mississippiense and H. ohiense type strains should be revisited with more representative samples from the genus.
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Affiliation(s)
- Colin S Maxwell
- Biology Department University of North Carolina Chapel Hill North Carolina 27599
| | - Victoria E Sepulveda
- Department of Microbiology and Immunology, School of Medicine University of North Carolina Chapel Hill North Carolina 27599
| | - David A Turissini
- Biology Department University of North Carolina Chapel Hill North Carolina 27599
| | - William E Goldman
- Department of Microbiology and Immunology, School of Medicine University of North Carolina Chapel Hill North Carolina 27599
| | - Daniel R Matute
- Biology Department University of North Carolina Chapel Hill North Carolina 27599
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20
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NLR surveillance of essential SEC-9 SNARE proteins induces programmed cell death upon allorecognition in filamentous fungi. Proc Natl Acad Sci U S A 2018; 115:E2292-E2301. [PMID: 29463729 DOI: 10.1073/pnas.1719705115] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In plants and metazoans, intracellular receptors that belong to the NOD-like receptor (NLR) family are major contributors to innate immunity. Filamentous fungal genomes contain large repertoires of genes encoding for proteins with similar architecture to plant and animal NLRs with mostly unknown function. Here, we identify and molecularly characterize patatin-like phospholipase-1 (PLP-1), an NLR-like protein containing an N-terminal patatin-like phospholipase domain, a nucleotide-binding domain (NBD), and a C-terminal tetratricopeptide repeat (TPR) domain. PLP-1 guards the essential SNARE protein SEC-9; genetic differences at plp-1 and sec-9 function to trigger allorecognition and cell death in two distantly related fungal species, Neurospora crassa and Podospora anserina Analyses of Neurospora population samples revealed that plp-1 and sec-9 alleles are highly polymorphic, segregate into discrete haplotypes, and show transspecies polymorphism. Upon fusion between cells bearing incompatible sec-9 and plp-1 alleles, allorecognition and cell death are induced, which are dependent upon physical interaction between SEC-9 and PLP-1. The central NBD and patatin-like phospholipase activity of PLP-1 are essential for allorecognition and cell death, while the TPR domain and the polymorphic SNARE domain of SEC-9 function in conferring allelic specificity. Our data indicate that fungal NLR-like proteins function similar to NLR immune receptors in plants and animals, showing that NLRs are major contributors to innate immunity in plants and animals and for allorecognition in fungi.
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21
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Bueno-Sancho V, Persoons A, Hubbard A, Cabrera-Quio LE, Lewis CM, Corredor-Moreno P, Bunting DCE, Ali S, Chng S, Hodson DP, Madariaga Burrows R, Bryson R, Thomas J, Holdgate S, Saunders DGO. Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity. Genome Biol Evol 2017; 9:3282-3296. [PMID: 29177504 PMCID: PMC5730935 DOI: 10.1093/gbe/evx241] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/27/2022] Open
Abstract
Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example, in the past two decades' wheat yellow (stripe) rust, Puccinia striiformis f. sp. tritici, has seen the emergence of new races that are adapted to warmer temperatures, have expanded virulence profiles, and are more aggressive than previous races, leading to wide-scale epidemics. Here, we used field-based genotyping to generate high-resolution data on P. striiformis genetics and carried out global population analysis. We also undertook comparative analysis of the 2014 and 2013 UK populations and assessed the temporal dynamics and host specificity of distinct pathogen genotypes. Our analysis revealed that P. striiformis lineages recently detected in Europe are extremely diverse and in fact similar to globally dispersed populations. In addition, we identified a considerable shift in the UK P. striiformis population structure including the first identification of one infamous race known as Kranich. Next, by establishing the genotype of both the pathogen and host within a single infected field sample, we uncovered evidence for varietal specificity for genetic groups of P. striiformis. Finally, we found potential seasonal specificity for certain genotypes of the pathogen with several lineages identified only in samples collected in late spring and into the summer, whereas one lineage was identified throughout the wheat growing season. Our discovery of which wheat varieties are susceptible to which specific P. striiformis isolates, and when those isolates are prevalent throughout the year, represents a powerful tool for disease management.
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Affiliation(s)
| | - Antoine Persoons
- Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom
| | - Amelia Hubbard
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Luis Enrique Cabrera-Quio
- Earlham Institute, Norwich Research Park, United Kingdom
- The Sainsbury Laboratory, Norwich Research Park, United Kingdom
| | - Clare M Lewis
- Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom
| | | | | | - Sajid Ali
- The University of Agriculture, Peshawar, Pakistan
| | - Soonie Chng
- The New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | | | | | - Rosie Bryson
- BASF SE, Agricultural Centre, Limburgerhof, Germany
| | - Jane Thomas
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Sarah Holdgate
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
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22
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Taylor JW, Branco S, Gao C, Hann-Soden C, Montoya L, Sylvain I, Gladieux P. Sources of Fungal Genetic Variation and Associating It with Phenotypic Diversity. Microbiol Spectr 2017; 5:10.1128/microbiolspec.funk-0057-2016. [PMID: 28936945 PMCID: PMC11687547 DOI: 10.1128/microbiolspec.funk-0057-2016] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 01/17/2023] Open
Abstract
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.
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Affiliation(s)
- John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102
| | - Sara Branco
- Département Génétique et Ecologie Evolutives Laboratoire Ecologie, Systématique et Evolution, CNRS-UPS-AgroParisTech, Université de Paris-Sud, 91405 Orsay, France, and Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717
| | - Cheng Gao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Chris Hann-Soden
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Iman Sylvain
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102
| | - Pierre Gladieux
- INRA, UMR BGPI, Campus International de Baillarguet, 34398 Montpellier, France
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23
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Branco S, Bi K, Liao HL, Gladieux P, Badouin H, Ellison CE, Nguyen NH, Vilgalys R, Peay KG, Taylor JW, Bruns TD. Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes. Mol Ecol 2017; 26:2063-2076. [PMID: 27761941 PMCID: PMC5392165 DOI: 10.1111/mec.13892] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 01/05/2023]
Abstract
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation.
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Affiliation(s)
- Sara Branco
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Ke Bi
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, Quincy FL 32351
| | | | - Hélène Badouin
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Christopher E. Ellison
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States of America
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
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Le Gac M, Metegnier G, Chomérat N, Malestroit P, Quéré J, Bouchez O, Siano R, Destombe C, Guillou L, Chapelle A. Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum. Mol Ecol 2016; 25:5129-5143. [DOI: 10.1111/mec.13815] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 01/07/2023]
Affiliation(s)
| | - Gabriel Metegnier
- Ifremer; DYNECO PELAGOS; 29280 Plouzané France
- CNRS, PUCCh, UACH, UMI 3614; Evolutionary Biology and Ecology of Algae; Station Biologique de Roscoff; Université Pierre et Marie Curie - Paris 6; Sorbonne Universités; Place Georges Teissier, CS90074 29688 Roscoff Cedex France
| | | | | | | | - Olivier Bouchez
- GeT PlaGe; Genotoul; INRA Auzeville; Castanet Tolosan France
| | | | - Christophe Destombe
- CNRS, PUCCh, UACH, UMI 3614; Evolutionary Biology and Ecology of Algae; Station Biologique de Roscoff; Université Pierre et Marie Curie - Paris 6; Sorbonne Universités; Place Georges Teissier, CS90074 29688 Roscoff Cedex France
| | - Laure Guillou
- CNRS, UMR 7144; Station Biologique de Roscoff; Université Pierre et Marie Curie - Paris 6; Sorbonne Universités; Place Georges Teissier CS90074 29688 Roscoff Cedex France
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Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever. mBio 2016; 7:e00550-16. [PMID: 27118594 PMCID: PMC4850269 DOI: 10.1128/mbio.00550-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Coccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region. Coccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis. The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii.
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Heller J, Zhao J, Rosenfield G, Kowbel DJ, Gladieux P, Glass NL. Characterization of Greenbeard Genes Involved in Long-Distance Kind Discrimination in a Microbial Eukaryote. PLoS Biol 2016; 14:e1002431. [PMID: 27077707 PMCID: PMC4831770 DOI: 10.1371/journal.pbio.1002431] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/11/2016] [Indexed: 01/09/2023] Open
Abstract
Microorganisms are capable of communication and cooperation to perform social activities. Cooperation can be enforced using kind discrimination mechanisms in which individuals preferentially help or punish others, depending on genetic relatedness only at certain loci. In the filamentous fungus Neurospora crassa, genetically identical asexual spores (germlings) communicate and fuse in a highly regulated process, which is associated with fitness benefits during colony establishment. Recognition and chemotropic interactions between isogenic germlings requires oscillation of the mitogen-activated protein kinase (MAPK) signal transduction protein complex (NRC-1, MEK-2, MAK-2, and the scaffold protein HAM-5) to specialized cell fusion structures termed conidial anastomosis tubes. Using a population of 110 wild N. crassa isolates, we investigated germling fusion between genetically unrelated individuals and discovered that chemotropic interactions are regulated by kind discrimination. Distinct communication groups were identified, in which germlings within one communication group interacted at high frequency, while germlings from different communication groups avoided each other. Bulk segregant analysis followed by whole genome resequencing identified three linked genes (doc-1, doc-2, and doc-3), which were associated with communication group phenotype. Alleles at doc-1, doc-2, and doc-3 fell into five haplotypes that showed transspecies polymorphism. Swapping doc-1 and doc-2 alleles from different communication group strains was necessary and sufficient to confer communication group affiliation. During chemotropic interactions, DOC-1 oscillated with MAK-2 to the tips of conidial anastomosis tubes, while DOC-2 was statically localized to the plasma membrane. Our data indicate that doc-1, doc-2, and doc-3 function as "greenbeard" genes, involved in mediating long-distance kind recognition that involves actively searching for one's own type, resulting in cooperation between non-genealogical relatives. Our findings serve as a basis for investigations into the mechanisms associated with attraction, fusion, and kind recognition in other eukaryotic species.
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Affiliation(s)
- Jens Heller
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | - Jiuhai Zhao
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | - Gabriel Rosenfield
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | - David J. Kowbel
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | | | - N. Louise Glass
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- * E-mail:
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The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa. mBio 2016; 7:e02148. [PMID: 26956589 PMCID: PMC4810495 DOI: 10.1128/mbio.02148-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Rapid responses to changes in incident light are critical to the guidance of behavior and development in most species. Phytochrome light receptors in particular play key roles in bacterial physiology and plant development, but their functions and regulation are less well understood in fungi. Nevertheless, genome-wide expression measurements provide key information that can guide experiments that reveal how genes respond to environmental signals and clarify their role in development. We performed functional genomic and phenotypic analyses of the two phytochromes in Neurospora crassa, a fungal model adapted to a postfire environment that experiences dramatically variable light conditions. Expression of phy-1 and phy-2 was low in early sexual development and in the case of phy-2 increased in late sexual development. Under light stimulation, strains with the phytochromes deleted exhibited increased expression of sexual development-related genes. Moreover, under red light, the phy-2 knockout strain commenced sexual development early. In the evolution of phytochromes within ascomycetes, at least two duplications have occurred, and the faster-evolving phy-2 gene has frequently been lost. Additionally, the three key cysteine sites that are critical for bacterial and plant phytochrome function are not conserved within fungal phy-2 homologs. Through the action of phytochromes, transitions between asexual and sexual reproduction are modulated by light level and light quality, presumably as an adaptation for fast asexual growth and initiation of sexual reproduction of N. crassa in exposed postfire ecosystems. Environmental signals, including light, play critical roles in regulating fungal growth and pathogenicity, and balance of asexual and sexual reproduction is critical in fungal pathogens’ incidence, virulence, and distribution. Red light sensing by phytochromes is well known to play critical roles in bacterial physiology and plant development. Homologs of phytochromes were first discovered in the fungal model Neurospora crassa and then subsequently in diverse other fungi, including many plant pathogens. Our study investigated the evolution of red light sensors in ascomycetes and confirmed—using the model fungus Neurospora crassa—their roles in modulating the asexual-sexual reproduction balance in fungi. Our findings also provide a key insight into one of the most poorly understood aspects of fungal biology, suggesting that further study of the function of phytochromes in fungi is critical to reveal the genetic basis of the asexual-sexual switch responsible for fungal growth and distribution, including diverse and destructive plant pathogens.
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Bruns TD, Taylor JW. Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism". Science 2016; 351:826. [DOI: 10.1126/science.aad4228] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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