1
|
Mbasa WV, Nene WA, Kapinga FA, Temu SG, Tibuhwa DD. Linking landscape habitats with prevalence of fusarium wilt disease of cashew crop in Tanzania. BMC Ecol Evol 2024; 24:101. [PMID: 39039497 DOI: 10.1186/s12862-024-02284-5] [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: 10/15/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Epidemic of Cashew Fusarium wilt disease (CFWD) has been a continuous focal challenge in the cashew farming, in Tanzania. Limited to edaphic conditions as a major factor in its epidemic, the current study aimed to assess the habitat-disease relationship. Purposive surveys involving assessment of disease prevalence and habitat compositions were conducted across four landscapes of southeastern zone from 2019 to 2023. Findings revealed a widespread of CFWD across diversified landscapes possessing varying habitat characteristics, mainly cultivated land with mature cashew, brownish sand loamy soils, grassland or shrub vegetation, seasonal river streamlines and natural water wells. The highest disease incidence and severity were noted at Nachingwea/Masasi plain (99.28:88.34%) followed by Liwale inland plain (98.64:89.3%), Coastal zone (72.72:59.83%) and Tunduru dissected plain (62.13:54.54%). The habitat characteristics were strongly similar within the landscape (0.86-Jaccard index) except between villages of the coastal zone (0.71-Jaccard index). Across landscapes, Nachingwea/Masasi plains and the Coastal zone were strongly similar to Tunduru dissected plain (0.63-1.0-Jaccard index), but strongly dissimilar with the Liwale inland plain (0.67-0.70- Jaccard distance). Furthermore, the presence of greater than 0.5 suitability indices across landscapes were revealed, with Liwale inland plain having strongest suitability index of 0.743 followed by Coastal zone (0.681), Tunduru dissected plain (0.617) and Nachingwea/Masasi plain. Significantly, the habitats had an increase of 0.1 suitability index, and positively correlated with disease prevalence by triggering disease incidence of 13.9% and severity of 31.4%. The study for the first time revealed the presence of an association between disease prevalence and landscape habitat characteristics of southeastern, Tanzania; paving the way to inclusive thinking of habitat as one of the drivers in the prevalence of fusarium wilt disease of cashews. Further research on the genetic coevolution of Fusarium oxysporum across landscapes to strengthen disease risk management in the cashew industry is recommended.
Collapse
Affiliation(s)
- William V Mbasa
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania.
- Tanzania Agricultural Research Institute-Naliendele, P.O. Box 509, Mtwara, Tanzania.
| | - Wilson A Nene
- Tanzania Agricultural Research Institute-Naliendele, P.O. Box 509, Mtwara, Tanzania
| | - Fortunus A Kapinga
- Tanzania Agricultural Research Institute-Naliendele, P.O. Box 509, Mtwara, Tanzania
| | - Stella G Temu
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Donatha D Tibuhwa
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| |
Collapse
|
2
|
Brejon Lamartinière E, Tremble K, Dentinger BTM, Dasmahapatra KK, Hoffman JI. Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis. Mol Ecol 2024:e17470. [PMID: 39034770 DOI: 10.1111/mec.17470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
Inbreeding, the mating of individuals that are related through common ancestry, is of central importance in evolutionary and conservation biology due to its impacts on individual fitness and population dynamics. However, while advanced genomic approaches have revolutionised the study of inbreeding in animals, genomic studies of inbreeding are rare in plants and lacking in fungi. We investigated global patterns of inbreeding in the prized edible porcini mushroom Boletus edulis using 225 whole genomes from seven lineages distributed across the northern hemisphere. Genomic inbreeding was quantified using runs of homozygosity (ROHs). We found appreciable variation both among and within lineages, with some individuals having over 20% of their genomes in ROHs. Much of this variation could be explained by a combination of elevation and latitude, and to a lesser extent by predicted habitat suitability during the last glacial maximum. In line with this, the majority of ROHs were short, reflecting ancient common ancestry dating back approximately 200-1700 generations ago, while longer ROHs indicative of recent common ancestry (less than approximately 50 generations ago) were infrequent. Our study reveals the inbreeding legacy of major climatic events in a widely distributed forest mutualist, aligning with prevailing theories and empirical studies of the impacts of historical glaciation events on the dominant forest tree species of the northern hemisphere.
Collapse
Affiliation(s)
- Etienne Brejon Lamartinière
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Keaton Tremble
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Bryn T M Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Natural History Museum of Utah, Salt Lake City, Utah, USA
| | | | - Joseph I Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Münster, Germany
- British Antarctic Survey, Cambridge, UK
| |
Collapse
|
3
|
Dan-Dan W, Jia-Jun N, Rui-Bian Z, Jie L, Yuan-Xu W, Liu Y, Fei-Fei C, Yue-Min P. A novel Burkholderia pyrrocinia strain effectively inhibits Fusarium graminearum growth and deoxynivalenol (DON) production. PEST MANAGEMENT SCIENCE 2024. [PMID: 38817082 DOI: 10.1002/ps.8200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/13/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Fusarium graminearum is a devastating fungal pathogen that poses a significant threat to global wheat production and quality. Control of this toxin-producing pathogen remains a major challenge. This study aimed to isolate strains with antagonistic activity against F. graminearum and at the same time to analyze the synthesis of deoxynivalenol (DON), in order to provide a new basis for the biological control of FHB. RESULTS Total of 69 microorganisms were isolated from the soil of a wheat-corn crop rotation field, and an antagonistic bacterial strain F12 was identified as Burkholderia pyrrocinia by molecular biology and carbon source utilization. F. graminearum control by strain F12 showed excellent biological activities under laboratory conditions (95.8%) and field testing (63.09%). Meanwhile, the DON content of field-treated wheat grains was detected the results showed that F12 have significantly inhibited of DON, which was further verified by qPCR that F12 produces secondary metabolites that inhibit the expression of DON and pigment-related genes. In addition, the sterile fermentation broth of F12 not only inhibited mycelial growth and spore germination, but also prevented mycelia from producing spores. CONCLUSION In this study B. pyrrocinia was reported to have good control of FHB and inhibition of DON synthesis. This novel B. pyrrocinia F12 is a promising biological inoculant, providing possibilities for controlling FHB, and a theoretical basis for the development of potential biocontrol agents and biofertilizers for agricultural use. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Wang Dan-Dan
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Laboratory of Mycology and Plant Fungal Diseases, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Nie Jia-Jun
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Zhao Rui-Bian
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Laboratory of Mycology and Plant Fungal Diseases, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Lu Jie
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wei Yuan-Xu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Laboratory of Mycology and Plant Fungal Diseases, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yu Liu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Chen Fei-Fei
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Laboratory of Mycology and Plant Fungal Diseases, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Pan Yue-Min
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Laboratory of Mycology and Plant Fungal Diseases, School of Plant Protection, Anhui Agricultural University, Hefei, China
| |
Collapse
|
4
|
Shigyo N, Umeki K, Hirao T. Soil microbial identity explains home-field advantage for litter decomposition. THE NEW PHYTOLOGIST 2024. [PMID: 38736202 DOI: 10.1111/nph.19769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/25/2024] [Indexed: 05/14/2024]
Abstract
Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.
Collapse
Affiliation(s)
- Nobuhiko Shigyo
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama, 368-0034, Japan
| | - Kiyoshi Umeki
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama, 368-0034, Japan
| |
Collapse
|
5
|
Ramírez Martínez J, Guillou S, Le Prieur S, Di Vittorio P, Bonal F, Taliadoros D, Gueret E, Fournier E, Stukenbrock EH, Valade R, Gladieux P. Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen. Microb Genom 2024; 10:001241. [PMID: 38713188 PMCID: PMC11170133 DOI: 10.1099/mgen.0.001241] [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: 12/21/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.
Collapse
Affiliation(s)
- Julie Ramírez Martínez
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | | | - Pauline Di Vittorio
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Florelle Bonal
- UMR AGAP (Amélioration génétique et adaptation des plantes), Montpellier, France
| | - Demetris Taliadoros
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | - Elise Gueret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Eva H. Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | | | - Pierre Gladieux
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
6
|
Adhikari TB, Olukolu BA, Paudel R, Pandey A, Halterman D, Louws FJ. Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato. PHYTOPATHOLOGY 2024; 114:653-661. [PMID: 37750924 DOI: 10.1094/phyto-07-23-0229-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.
Collapse
Affiliation(s)
- Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Bode A Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996
| | - Rajan Paudel
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
| | - Anju Pandey
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695
| |
Collapse
|
7
|
Del Grosso C, Palmieri D, Marchese L, Melissano L, Lima G. First Report of Diplodia quercivora and Neofusicoccum vitifusiforme Associated with Cankers and Necrosis of Holm Oak ( Quercus ilex) in Declining Stands in Southern Italy. J Fungi (Basel) 2024; 10:35. [PMID: 38248945 PMCID: PMC10820903 DOI: 10.3390/jof10010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
The emergence of new plant diseases is an increasingly important concern. Climate change is likely to be among the factors causing most of the emerging diseases endangering forest and tree heritage around the world. Such diseases may be caused by latent pathogens or microorganisms cryptically associated with plants. The shift from a non-pathogenic to a pathogenic stage may depend on physiological alterations of the host, environmental changes, and/or stress factors. In some woods of the Salento Peninsula (Apulia Region, Italy), sudden declines of holm oak plants (Quercus ilex L.) have been observed since 2016. The morphological and molecular characterization of representative fungal isolates associated with cankers and necrosis in declining plants indicated that these isolates belong to the Botryosphaeriaceae family, and the most frequent species were Diplodia corticola and Diplodia quercivora, followed by Neofusicoccum vitifusiforme. In artificially inoculated young holm oak plants, both D. corticola and D. quercivora species produced intense and severe subcortical and leaf margin necrosis. N. vitifusiforme, although less aggressive, induced the same symptoms. Our research, in addition to confirming the involvement of D. corticola in olm oak decline, represents the first report of D. quercivora as a new pathogen of Q. ilex in Italy. Furthermore, to the best of our knowledge, we also found N. vitifusiforme as a new pathogen of Q. ilex.
Collapse
Affiliation(s)
- Carmine Del Grosso
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
- Institute for Sustainable Plant Protection, National Research Council (CNR), 70126 Bari, Italy
| | - Davide Palmieri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
| | - Lucia Marchese
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
| | - Luigi Melissano
- Department of Agriculture, Environment and Rural Development, Sustainable Management and Protection of Natural and Forest Resources, Apulia Region, 70100 Bari, Italy;
| | - Giuseppe Lima
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy; (D.P.); (L.M.)
| |
Collapse
|
8
|
Subedi A, Barrera LBTDL, Ivey ML, Egel DS, Kebede M, Kara S, Aysan Y, Minsavage GV, Roberts PD, Jones JB, Goss EM. Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper. PHYTOPATHOLOGY 2024; 114:241-250. [PMID: 37432099 DOI: 10.1094/phyto-04-23-0128-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Xanthomonas perforans-the dominant causal agent of bacterial leaf spot of tomato-is an emerging pathogen of pepper, indicative of a potential host expansion across the southeastern United States. However, studies of the genetic diversity and evolution of X. perforans from pepper remain limited. In this study, the whole-genome sequences of 35 X. perforans strains isolated from pepper from four fields and two transplant facilities across southwest Florida between 2019 and 2021 were used to compare genomic divergence, evolution, and variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all 35 X. perforans strains formed one genetic cluster with pepper and tomato strains from Alabama and Turkey and were closely related to strains isolated from tomato in Indiana, Mexico, and Louisiana. The in planta population growth of tomato strains isolated from Indiana, Mexico, Louisiana, and Turkey in pepper leaf mesophyll was on par with pepper X. perforans and X. euvesicatoria strains. Molecular clock analysis of the 35 Florida strains dated their emergence to approximately 2017. While strains varied in copper tolerance, all sequenced strains harbored the avrHah1 transcription activation-like effector located on a conjugative plasmid, not previously reported in Florida. Our findings suggest that there is a geographically distributed lineage of X. perforans strains on tomato that has the genetic background to cause disease on pepper. Moreover, this study clarifies potential adaptive variants of X. perforans on pepper that could help forecast the emergence of such strains and enable immediate or preemptive intervention.
Collapse
Affiliation(s)
- Aastha Subedi
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | | | - Melanie Lewis Ivey
- Department of Plant Pathology, The Ohio State University, Wooster, OH, U.S.A
| | - Daniel S Egel
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN, U.S.A
| | - Misrak Kebede
- Biotechnology Department, Collage of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Serhat Kara
- Alata Horticulture Research Institute, Mersin, Turkey
| | - Yesim Aysan
- Department of Plant Protection, Cukurova University, Adana, Turkey
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Pamela D Roberts
- Southwest Florida Research & Education Center, University of Florida, Immokalee, FL, U.S.A
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| |
Collapse
|
9
|
Du H, Gao F, Yang S, Zhu H, Cheng C, Peng F, Zhang W, Zheng Z, Wang X, Yang Y, Hou W. Oxidized of chitosan with different molecular weights for potential antifungal and plant growth regulator applications. Int J Biol Macromol 2023; 253:126862. [PMID: 37703971 DOI: 10.1016/j.ijbiomac.2023.126862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023]
Abstract
The application of Chitosan (CS) in drug delivery systems, plant growth promotion, antibacterial potentiality and plant defense is significantly limited by its inability to dissolve in neutral solutions. In this work, CS with different molecular weights (Mw) has been oxidized, yielding five kinds of oxidized chitosan (OCS 1-5) with solubilities in neutral solutions. The results obtained from Fourier Transform Infrared Spectroscopy clearly showed the successful oxidation of the hydroxyl group to form aldehyde and carboxyl groups. And the CS derivatives showed the wrinkled and lamellar structures on the surface of OCS. The results of antifungal activity against Fusarium graminearum showed that the OCS dissolved in 2 % (V/V) acetic acid exhibited better performance of almost complete inhibition of mycelial growth compared with CS at the concentration of 500 μg/mL. Among the five OCS, OCS-4 exhibited the best antifungal effect and had the lowest EC50 value of 581.68 μg/mL in samples. OCS-4 displayed superior promoting effect on seed germination with a germination potential of 62.2 % at a concentration of 3 g/L and a germination rate of 74.5 %. Additionally, the other four OCS also showed excellent antifungal activity with dose-dependent manners. These results indicated that the OCS had excellent antifungal potential in agricultural production.
Collapse
Affiliation(s)
- Haoyang Du
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; College of Chemical Engineering, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Fengkun Gao
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; College of Chemical Engineering, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Shu Yang
- College of Chemical Engineering, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Hongxia Zhu
- College of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, PR China
| | - Caihong Cheng
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; Analysis and Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Fei Peng
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; Analysis and Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Wenjing Zhang
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; College of Chemical Engineering, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Zhe Zheng
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; College of Chemical Engineering, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China
| | - Xiuping Wang
- Analysis and Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China.
| | - Yuedong Yang
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China.
| | - Wenlong Hou
- Hebei Key Laboratory of Active Components and Functions in Natural Products, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China; Analysis and Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao 066000, China.
| |
Collapse
|
10
|
Khan S, Srivastava S, Karnwal A, Malik T. Streptomyces as a promising biological control agents for plant pathogens. Front Microbiol 2023; 14:1285543. [PMID: 38033592 PMCID: PMC10682734 DOI: 10.3389/fmicb.2023.1285543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Plant diseases caused by pathogenic microorganisms in agriculture present a considerable obstacle, resulting in approximately 30-40% crop damage. The use of conventional techniques to manage these microorganisms, i.e., applying chemical pesticides and antimicrobials, has been discovered to have adverse effects on human health and the environment. Furthermore, these methods have contributed to the emergence of resistance among phytopathogens. Consequently, it has become imperative to investigate natural alternatives to address this issue. The Streptomyces genus of gram-positive bacteria is a potentially viable natural alternative that has been extensively researched due to its capacity to generate diverse antimicrobial compounds, such as metabolites and organic compounds. Scientists globally use diverse approaches and methodologies to extract new bioactive compounds from these bacteria. The efficacy of bioactive compounds in mitigating various phytopathogens that pose a significant threat to crops and plants has been demonstrated. Hence, the Streptomyces genus exhibits potential as a biological control agent for combating plant pathogens. This review article aims to provide further insight into the Streptomyces genus as a source of antimicrobial compounds that can potentially be a biological control against plant pathogens. The investigation of various bioactive compounds synthesized by this genus can enhance our comprehension of their prospective utilization in agriculture.
Collapse
Affiliation(s)
- Shaista Khan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Seweta Srivastava
- School of Agriculture, Lovely Professional University, Phagwara, Punjab, India
| | - Arun Karnwal
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Department of Biomedical sciences, Jimma University, Jimma, Ethiopia
| |
Collapse
|
11
|
Tanaka E, Tanada K, Hosoe T, Shrestha B, Kolařík M, Liu M. In search of lost ergots: phylogenetic re-evaluation of Claviceps species in Japan and their biogeographic patterns revealed. Stud Mycol 2023; 106:1-39. [PMID: 38298573 PMCID: PMC10825747 DOI: 10.3114/sim.2023.106.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 02/02/2024] Open
Abstract
Claviceps (Clavicipitaceae, Hypocreales) was erected in 1853, although ergotism had been well-known for a much longer time. By 2000, about 70 taxa had been described in Claviceps, of which eight species and six varieties were based on Japanese type or authentic specimens. Most of these Japanese Claviceps taxa are based on lost specimens or have invalid names, which means many species practically exist only in the scientific literature. The ambiguous identities of these species have hindered taxonomic resolution of the genus Claviceps. Consequently, we sought and collected more than 300 fresh specimens in search of the lost Japanese ergots. Multilocus phylogenetic analyses based on DNA sequences from LSU, TEF-1α, TUB2, Mcm7, and RPB2 revealed the phylogenetic relationships between the Japanese specimens and known Claviceps spp., as well as the presence of biogeographic patterns. Based on the phylogenetic analysis, host range and morphology, we re-evaluated Japanese Claviceps and recognised at least 21 species in Japan. Here we characterised 14 previously described taxa and designated neo-, lecto- and epi-types for C. bothriochloae, C. imperatae, C. litoralis, C. microspora, C. panicoidearum and C. yanagawaensis. Two varieties were elevated to species rank with designated neotypes, i.e. C. agropyri and C. kawatanii. Six new species, C. miscanthicola, C. oplismeni, C. palustris, C. phragmitis, C. sasae and C. tandae were proposed and described. Taxonomic novelties: New species: Claviceps miscanthicola E. Tanaka, Claviceps oplismeni E. Tanaka, Claviceps palustris E. Tanaka, Claviceps phragmitis E. Tanaka, Claviceps sasae E. Tanaka, Claviceps tandae E. Tanaka; New status and combination: Claviceps agropyri (Tanda) E. Tanaka, Claviceps kawatanii (Tanda) E. Tanaka; Typifications (basionyms): Lecto- and epitypification: Claviceps yanagawaensis Togashi; Neotypifications: Claviceps purpurea var. agropyri Tanda, Claviceps bothriochloae Tanda & Y. Muray, Claviceps imperatae Tanda & Kawat., Claviceps microspora var. kawatanii Tanda, Claviceps litoralis Kawat., Claviceps microspora Tanda, Claviceps panicoidearum Tanda & Y. Harada; Resurrection: Claviceps queenslandica Langdon. Citation: Tanaka E, Tanada K, Hosoe T, Shrestha B, Kolařík M, Liu M (2023). In search of lost ergots: phylogenetic re-evaluation of Claviceps species in Japan and their biogeographic patterns revealed. Studies in Mycology 106: 1-39. doi: 10.3114/sim.2022.106.01.
Collapse
Affiliation(s)
- E. Tanaka
- Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - K. Tanada
- Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | - T. Hosoe
- Department of Organic Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan
| | - B. Shrestha
- Madan Bhandari University of Science and Technology, Saibu, Bhaisepati, Lalitpur, Nepal
| | - M. Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - M. Liu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A0C6, Canada
| |
Collapse
|
12
|
Maguvu TE, Travadon R, Cantu D, Trouillas FP. Whole genome sequencing and analysis of multiple isolates of Ceratocystis destructans, the causal agent of Ceratocystis canker of almond in California. Sci Rep 2023; 13:14873. [PMID: 37684350 PMCID: PMC10491840 DOI: 10.1038/s41598-023-41746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Ceratocystis canker caused by Ceratocystis destructans is a severe disease of almond, reducing the longevity and productivity of infected trees. Once the disease has established in an individual tree, there is no cure, and management efforts are often limited to removing the infected area of cankers. In this study, we present the genome assemblies of five C. destructans isolates isolated from symptomatic almond trees. The genomes were assembled into a genome size of 27.2 ± 0.9 Mbp with an average of 6924 ± 135 protein-coding genes and an average GC content of 48.8 ± 0.02%. We concentrated our efforts on identifying putative virulence factors of canker pathogens. Analysis of the secreted carbohydrate-active enzymes showed that the genomes harbored 83.4 ± 1.8 secreted CAZymes. The secreted CAZymes covered all the known categories of CAZymes. AntiSMASH revealed that the genomes had at least 7 biosynthetic gene clusters, with one of the non-ribosomal peptide synthases encoding dimethylcoprogen, a conserved virulence determinant of plant pathogenic ascomycetes. From the predicted proteome, we also annotated cytochrome P450 monooxygenases, and transporters, these are well-established virulence determinants of canker pathogens. Moreover, we managed to identify 57.4 ± 2.1 putative effector proteins. Gene Ontology (GO) annotation was applied to compare gene content with two closely related species C. fimbriata, and C. albifundus. This study provides the first genome assemblies for C. destructans, expanding genomic resources for an important almond canker pathogen. The acquired knowledge provides a foundation for further advanced studies, such as molecular interactions with the host, which is critical for breeding for resistance.
Collapse
Affiliation(s)
- Tawanda E Maguvu
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
- Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, CA, 95616, USA
| | - Florent P Trouillas
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
- Kearney Agricultural Research and Extension Center, Parlier, CA, 93648, USA.
| |
Collapse
|
13
|
D'Bastiani E, Princepe D, Marquitti FMD, Boeger WA, Campião KM, Araujo SBL. Effect of Host-Switching on the Ecological and Evolutionary Patterns of Parasites. Syst Biol 2023; 72:912-924. [PMID: 37097763 DOI: 10.1093/sysbio/syad022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Speciation via host-switching is a macroevolutionary process that emerges from a microevolutionary dynamic where individual parasites switch hosts, establish a new association, and reduce reproductive contact with the original parasite lineage. Phylogenetic distance and geographic distribution of the hosts have been shown to be determinants of the capacity and opportunity of the parasite to change hosts. Although speciation via host-switching has been reported in many host-parasite systems, its dynamic on the individual, population and community levels is poorly understood. Here we propose a theoretical model to simulate parasite evolution considering host-switching events on the microevolutionary scale, taking into account the macroevolutionary history of the hosts, to evaluate how host-switching can affect ecological and evolutionary patterns of parasites in empirical communities at regional and local scales. In the model, parasite individuals can switch hosts under variable intensity and have their evolution driven by mutation and genetic drift. Mating is sexual and only individuals that are sufficiently similar can produce offspring. We assumed that parasite evolution occurs at the same evolutionary time scale as their hosts, and that the intensity of host-switching decreases as the host species differentiate. Ecological and evolutionary patterns were characterized by the turnover of parasite species among host species, and parasite evolutionary tree imbalance respectively. We found a range of host-switching intensity that reproduces ecological and evolutionary patterns observed in empirical communities. Our results showed that turnover decreased as host-switching intensity increased, with low variation among the model replications. On the other hand, tree imbalance showed wide variation and non-monotonic tendency. We concluded that tree imbalance was sensitive to stochastic events, whereas turnover may be a good indicator of host-switching. We found that local communities corresponded to higher host-switching intensity when compared to regional communities, highlighting that spatial scale is a limitation for host-switching. [Dispersal of parasites, opportunity and capacity of interaction, phylogenetic conservatism, and community structure.].
Collapse
Affiliation(s)
- Elvira D'Bastiani
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| | - Débora Princepe
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, UNICAMP-Campinas, São Paulo, Brasil
| | - Flavia M D Marquitti
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, UNICAMP-Campinas, São Paulo, Brasil
- Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP-Campinas, São Paulo, Brasil
| | - Walter A Boeger
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
- Departamento de Zoologia, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| | - Karla M Campião
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
- Departamento de Zoologia, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| | - Sabrina B L Araujo
- Laboratório de Interações Biológicas, Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
- Departamento de Física, Universidade Federal do Paraná, UFPR-Curitiba, Paraná, Brasil
| |
Collapse
|
14
|
Ndinga-Muniania C, Wornson N, Fulcher MR, Borer ET, Seabloom EW, Kinkel L, May G. Cryptic functional diversity within a grass mycobiome. PLoS One 2023; 18:e0287990. [PMID: 37471328 PMCID: PMC10358963 DOI: 10.1371/journal.pone.0287990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 07/22/2023] Open
Abstract
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
Collapse
Affiliation(s)
- Cedric Ndinga-Muniania
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nicholas Wornson
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael R Fulcher
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Linda Kinkel
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| |
Collapse
|
15
|
Feau N, Dhillon BD, Sakalidis M, Dale AL, Søndreli KL, Goodwin SB, LeBoldus JM, Hamelin RC. Forest health in the Anthropocene: the emergence of a novel tree disease is associated with poplar cultivation. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220008. [PMID: 36744569 PMCID: PMC9900707 DOI: 10.1098/rstb.2022.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Plant domestication and movement are large contributors to the success of new diseases. The introduction of new host species can result in accelerated evolutionary changes in pathogens, affecting long-established coevolutionary dynamics. This has been observed in poplars where severe epidemics of pathogens that were innocuous in their natural pathosystems occurred following host domestication. The North American fungus Sphaerulina musiva is responsible for endemic leaf spots on Populus deltoides. We show that the expansion of poplar cultivation resulted in the emergence of a new lineage of this pathogen that causes stem infections on a new host, P. balsamifera. This suggests a host shift since this is not a known host. Genome analysis of this emerging lineage reveals a mosaic pattern with islands of diversity separated by fixed genome regions, which is consistent with a homoploid hybridization event between two individuals that produced a hybrid swarm. Genome regions of extreme divergence and low diversity are enriched in genes involved in host-pathogen interactions. The specialization of this emerging lineage to a new host and its clonal propagation represents a serious threat to poplars and could affect both natural and planted forests. This work provides a clear example of the changes created by the intensification of tree cultivation that facilitate the emergence of specialized pathogens, jeopardizing the natural equilibrium between hosts and pathogens. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
Collapse
Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada, V8Z 1M5
| | - Braham D. Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Department of Plant Pathology, University of Florida - Fort Lauderdale Research and Education Center, Davie, FL 33314, USA
| | - Monique Sakalidis
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA,Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,GC-New Construction Materials, FPInnovations, Vancouver, BC, Canada, V6T 1Z4
| | - Kelsey L. Søndreli
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Jared M. LeBoldus
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA,Forest Engineering, Resources and Management Department, Oregon State University, Corvallis, OR 97331, USA
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada, G1V 0A6
| |
Collapse
|
16
|
Kong P, Daughtrey ML, Hong C. Differential Adaptation Has Resulted in Aggressiveness Variation of Calonectria pseudonaviculata on Hosts Buxus, Pachysandra, and Sarcococca. J Fungi (Basel) 2023; 9:jof9020181. [PMID: 36836296 PMCID: PMC9966688 DOI: 10.3390/jof9020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Calonectria pseudonaviculata (Cps) infects Buxus (boxwood), Pachysandra (pachysandra), and Sarcococca spp. (sweet box); yet, how it adapts to its hosts has been unclear. Here, we performed serial passage experiments with the three hosts and measured Cps changes in three aggressiveness components: infectibility, lesion size, and conidial production. The detached leaves of individual hosts were inoculated with isolates (P0) from the originating host, followed by nine serial inoculations of new leaves of the same host with conidia from the infected leaves of the previous inoculation. All boxwood isolates maintained their capability of infection and lesion expansion through the 10 passages, whereas most non-boxwood isolates lost these abilities during the passages. Isolates from plants of origin (*-P0) and their descendants isolated from passages 5 (*-P5) and 10 (*-P10) were used to evaluate aggressiveness changes on all three hosts with cross-inoculation. While post-passage boxwood isolates gave enlarged lesions on pachysandra, sweet box P5 and pachysandra P10 isolates showed reduced aggressiveness on all hosts. Cps appears to be most adapted to boxwood and less adapted to sweet box and pachysandra. These results suggest speciation of Cps, with its coevolutionary pace with the hosts the fastest with boxwood, intermediate with sweet box, and the slowest with pachysandra.
Collapse
Affiliation(s)
- Ping Kong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
- Correspondence:
| | - Margery L. Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, NY 11901, USA
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| |
Collapse
|
17
|
Bazzicalupo A. Local adaptation in fungi. FEMS Microbiol Rev 2022; 46:6604384. [PMID: 35675293 DOI: 10.1093/femsre/fuac026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
In this review, I explore the pervasive but underappreciated role of local adaptation in fungi. It has been difficult historically to study local adaptation in fungi because of the limited understanding of fungal species and their traits, but new hope has been offered with technological advances in sequencing. The filamentous nature of fungi invalidates some assumptions made in evolution because of their ability to exist as multinucleate entities with genetically different nuclei sharing the same cytoplasm. Many insights on local adaptation have come from studying fungi, and much of the empirical evidence gathered about local adaptation in the context of host-pathogen interactions comes from studying fungal virulence genes, drug resistance, and environmental adaptation. Together, these insights paint a picture of the variety of processes involved in fungal local adaptation and their connections to the unusual cell biology of Fungi (multinucleate, filamentous habit), but there is much that remains unknown, with major gaps in our knowledge of fungal species, their phenotypes, and the ways by which they adapt to local conditions.
Collapse
Affiliation(s)
- Anna Bazzicalupo
- Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., Vancouver V6T 1Z4, Canada
| |
Collapse
|
18
|
Leuchtmann A, Schardl CL. Genetic Diversity of Epichloë Endophytes Associated with Brachypodium and Calamagrostis Host Grass Genera including Two New Species. J Fungi (Basel) 2022; 8:jof8101086. [PMID: 36294651 PMCID: PMC9605649 DOI: 10.3390/jof8101086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Fungi of genus Epichloë (Ascomycota, Clavicipitaceae) are common endophytic symbionts of Poaceae, including wild and agronomically important cool-season grass species (subfam. Poöideae). Here, we examined the genetic diversity of Epichloë from three European species of Brachypodium (B. sylvaticum, B. pinnatum and B. phoenicoides) and three species of Calamagrostis (C. arundinacea, C. purpurea and C. villosa), using DNA sequences of tubB and tefA genes. In addition, microsatellite markers were obtained from a larger set of isolates from B. sylvaticum sampled across Europe. Based on phylogenetic analyses the isolates from Brachypodium hosts were placed in three different subclades within the Epichloë typhina complex (ETC) but did not strictly group according to host grass species, suggesting that the host does not always select for particular endophyte genotypes. Analysis of microsatellite markers confirmed the presence of genetically distinct lineages of Epichloësylvatica on B. sylvaticum, which appeared to be tied to different modes of reproduction (sexual or asexual). Among isolates from Calamagrostis hosts, two subclades were detected which were placed outside ETC. These endophyte lineages are recognized as distinct species for which we propose the names E. calamagrostidis Leuchtm. & Schardl, sp. nov. and E. ftanensis Leuchtm. & A.D. Treindl, sp. nov. This study extends knowledge of the phylogeny and evolutionary diversification of Epichloë endophytes that are symbionts of wild Brachypodium and Calamagrostis host grasses.
Collapse
Affiliation(s)
- Adrian Leuchtmann
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zürich, Switzerland
- Correspondence:
| | | |
Collapse
|
19
|
Kumari D, Prasad BD, Dwivedi P, Hidangmayum A, Sahni S. CRISPR/Cas9 mediated genome editing tools and their possible role in disease resistance mechanism. Mol Biol Rep 2022; 49:11587-11600. [DOI: 10.1007/s11033-022-07851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/14/2022] [Accepted: 08/08/2022] [Indexed: 10/14/2022]
|
20
|
Batool W, Liu C, Fan X, Zhang P, Hu Y, Wei Y, Zhang SH. AGC/AKT Protein Kinase SCH9 Is Critical to Pathogenic Development and Overwintering Survival in Magnaporthe oryzae. J Fungi (Basel) 2022; 8:jof8080810. [PMID: 36012798 PMCID: PMC9410157 DOI: 10.3390/jof8080810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/06/2023] Open
Abstract
Primary inoculum that survives overwintering is one of the key factors that determine the outbreak of plant disease. Pathogenic resting structures, such as chlamydospores, are an ideal inoculum for plant disease. Puzzlingly, Magnaporthe oryzae, a devastating fungal pathogen responsible for blast disease in rice, hardly form any morphologically changed resting structures, and we hypothesize that M. oryzae mainly relies on its physiological alteration to survive overwintering or other harsh environments. However, little progress on research into regulatory genes that facilitate the overwintering of rice blast pathogens has been made so far. Serine threonine protein kinase AGC/AKT, MoSch9, plays an important role in the spore-mediated pathogenesis of M. oryzae. Building on this finding, we discovered that in genetic and biological terms, MoSch9 plays a critical role in conidiophore stalk formation, hyphal-mediated pathogenesis, cold stress tolerance, and overwintering survival of M. oryzae. We discovered that the formation of conidiophore stalks and disease propagation using spores was severely compromised in the mutant strains, whereas hyphal-mediated pathogenesis and the root infection capability of M. oryzae were completely eradicated due to MoSch9 deleted mutants’ inability to form an appressorium-like structure. Most importantly, the functional and transcriptomic study of wild-type and MoSch9 mutant strains showed that MoSch9 plays a regulatory role in cold stress tolerance of M. oryzae through the transcription regulation of secondary metabolite synthesis, ATP hydrolyzing, and cell wall integrity proteins during osmotic stress and cold temperatures. From these results, we conclude that MoSch9 is essential for fungal infection-related morphogenesis and overwintering of M. oryzae.
Collapse
|
21
|
Thierry M, Charriat F, Milazzo J, Adreit H, Ravel S, Cros-Arteil S, borron S, Sella V, Kroj T, Ioos R, Fournier E, Tharreau D, Gladieux P. Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities. PLoS Pathog 2022; 18:e1010687. [PMID: 35877779 PMCID: PMC9352207 DOI: 10.1371/journal.ppat.1010687] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/04/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
Collapse
Affiliation(s)
- Maud Thierry
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Joëlle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia borron
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Violaine Sella
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- * E-mail: (DT); (PG)
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- * E-mail: (DT); (PG)
| |
Collapse
|
22
|
Na DH, Lee JS, Shin HD, Ono Y, Choi YJ. Emergence of a New Rust Disease of Virginia Creeper ( Parthenocissus quinquefolia) through a Host Range Expansion of Neophysopella vitis. MYCOBIOLOGY 2022; 50:166-171. [PMID: 37969690 PMCID: PMC10635169 DOI: 10.1080/12298093.2022.2076366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2023]
Abstract
Virginia creeper (or five-leaved ivy; Parthenocissus quinquefolia) is one of the most popular and widely grown climbers worldwide. In September 2021, Virginia creeper leaves with typical rust symptom were found in an arboretum in Korea, with severe damage. Globally, there is no record of a rust disease on Virginia creeper. Using morphological investigation and molecular phylogenetic inferences, the rust agent was identified as Neophysopella vitis, which is a rust pathogen of other Parthenocissus spp. including Boston ivy (P. tricuspidata). Given that the two ivy plants, Virginia creeper and Boston ivy, have common habitats, especially on buildings and walls, throughout Korea, and that N. vitis is a ubiquitous rust species affecting Boston ivy in Korea, it is speculated that the host range of N. vitis may recently have expanded from Boston ivy to Virginia creeper. The present study reports a globally new rust disease on Virginia creeper, which could be a major threat to the ornamental creeper.
Collapse
Affiliation(s)
- Dong-Hwan Na
- Department of Biological Science, Kunsan National University, Gunsan, Korea
| | - Jae Sung Lee
- Department of Biological Science, Kunsan National University, Gunsan, Korea
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Yoshitaka Ono
- College of Education, Ibaraki University, Ibaraki, Japan
| | - Young-Joon Choi
- Department of Biological Science, Kunsan National University, Gunsan, Korea
| |
Collapse
|
23
|
López-Estrada EK, Sanmartín I, Uribe JE, Abalde S, Jiménez-Ruiz Y, García-París M. Mitogenomics and hidden-trait models reveal the role of phoresy and host shifts in the diversification of parasitoid blister beetles (Coleoptera: Meloidae). Mol Ecol 2022; 31:2453-2474. [PMID: 35146829 PMCID: PMC9305437 DOI: 10.1111/mec.16390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022]
Abstract
Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the consequences of changes in two life history traits, host‐type and phoresy, in the hypermetamorphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most genera and tribes are bee‐parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diversification rates and changes in host specificity and phoresy, using state‐dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic‐taxonomic approach based on birth‐death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermetamorphic Meloidae was a nonphoretic bee‐parasitoid, and that transitions towards a phoretic bee‐parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee‐parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee‐and grasshopper‐parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary success of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversification dynamics.
Collapse
Affiliation(s)
- E K López-Estrada
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España.,Real Jardín Botánico (RJB-CSIC). Plaza de Murillo, 2, 28014. Madrid, España
| | - I Sanmartín
- Real Jardín Botánico (RJB-CSIC). Plaza de Murillo, 2, 28014. Madrid, España
| | - J E Uribe
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| | - S Abalde
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España.,Centro de Estudios Avanzados de Blanes (CEAB-CSIC). Accéss, Cala Sant Francesc, 14, 17300, Blanes, España
| | - Y Jiménez-Ruiz
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| | - M García-París
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, 28006, Madrid, España
| |
Collapse
|
24
|
Castillo AI, Tsai CW, Su CC, Weng LW, Lin YC, Cho ST, Almeida RPP, Kuo CH. Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan. Microb Genom 2021; 7. [PMID: 34898423 PMCID: PMC8767338 DOI: 10.1099/mgen.0.000727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce’s disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis, which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.
Collapse
Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chi-Wei Tsai
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chiou-Chu Su
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Taichung 413, Taiwan, ROC
| | - Ling-Wei Weng
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| |
Collapse
|
25
|
Liu Y, Duan D, Jiang F, Tian Z, Feng X, Wu N, Hou F, Kardol P, Nan Z, Chen T. Long‐term heavy grazing increases community‐level foliar fungal diseases by shifting plant composition. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Liu
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
- Industrial Crop Research Institute of Sichuan Academy of Agricultural Sciences Chengdu China
| | - Dongdong Duan
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Feifei Jiang
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Zhen Tian
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Xiaoxuan Feng
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Nana Wu
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Paul Kardol
- Department of Forest Ecology and Management Swedish University of Agricultural Sciences Umeå Sweden
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| | - Tao Chen
- State Key Laboratory of Grassland Agro‐ecosystems Center for Grassland Microbiome College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China
| |
Collapse
|
26
|
Kobmoo N, Arnamnart N, Pootakham W, Sonthirod C, Khonsanit A, Kuephadungphan W, Suntivich R, Mosunova O, Giraud T, Luangsa-ard J. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. PERSOONIA 2021; 47:136-150. [PMID: 37693793 PMCID: PMC10486633 DOI: 10.3767/persoonia.2021.47.04] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/12/2021] [Indexed: 11/25/2022]
Abstract
Fungi are rich in complexes of cryptic species that need a combination of different approaches to be delimited, including genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. In this study we present a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana s.lat. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and among three clades in B. bassiana, supporting their subdivision as distinct species. Morphological examination focusing on the width and the length of phialides and conidia showed no difference among the clades within B. bassiana while conidial length was significantly different among clades within B. asiatica. The secondary metabolite profiles obtained by liquid chromatography-mass spectrometry (LC-MS) allowed a distinction between B. asiatica and B. bassiana, but not between the clades therein. Based on these genomic, morphological, chemical data, we proposed a clade of B. asiatica as a new species, named B. thailandica, and two clades of B. bassiana to respectively represent B. namnaoensis and B. neobassiana spp. nov. Such closely related but divergent species with different host ranges have potential to elucidate the evolution of host specificity, with potential biocontrol application. Citation: Kobmoo N, Arnamnart N, Pootakham W, et al. 2021. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia 47: 136-150. https://doi.org/10.3767/persoonia.2021.47.04.
Collapse
Affiliation(s)
- N. Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - N. Arnamnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - W. Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - C. Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - A. Khonsanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - W. Kuephadungphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - R. Suntivich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - O.V. Mosunova
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Giraud
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - J.J. Luangsa-ard
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
27
|
Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. PHYTOPATHOLOGY 2021; 111:2355-2366. [PMID: 33829853 DOI: 10.1094/phyto-07-20-0302-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help to prevent the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the gray mold pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host of origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and nonsynonymous sites, and analyses of presence and absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.
Collapse
Affiliation(s)
- Alex Mercier
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
- Université Paris-Saclay, Orsay, France
| | - Adeline Simon
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Marc Bardin
- UR0407 Pathologie Végétale, INRAE, 84143 Montfavet, France
| | - Anne-Sophie Walker
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Muriel Viaud
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
28
|
Gougherty AV, Davies TJ. Towards a phylogenetic ecology of plant pests and pathogens. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200359. [PMID: 34538142 PMCID: PMC8450633 DOI: 10.1098/rstb.2020.0359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2021] [Indexed: 01/17/2023] Open
Abstract
Plant-pathogens and insect pests, hereafter pests, play an important role in structuring ecological communities, yet both native and introduced pests impose significant pressure on wild and managed systems, and pose a threat to food security. Global changes in climate and land use, and transportation of plants and pests around the globe are likely to further increase the range, frequency and severity of pest outbreaks in the future. Thus, there is a critical need to expand on current ecological theory to address these challenges. Here, we outline a phylogenetic framework for the study of plant and pest interactions. In plants, a growing body of work has suggested that evolutionary relatedness, phylogeny, strongly structures plant-pest associations-from pest host breadths and impacts, to their establishment and spread in new regions. Understanding the phylogenetic dimensions of plant-pest associations will help to inform models of invasive species spread, disease and pest risk in crops, and emerging pest outbreaks in native plant communities-which will have important implications for protecting food security and biodiversity into the future. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
Collapse
Affiliation(s)
- Andrew V. Gougherty
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - T. Jonathan Davies
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2092, South Africa
| |
Collapse
|
29
|
Kobmoo N, Arnamnart N, Pootakham W, Sonthirod C, Khonsanit A, Kuephadungphan W, Suntivich R, Mosunova O, Giraud T, Luangsa-ard J. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. PERSOONIA 2021; 47:136-150. [PMID: 38352976 PMCID: PMC10784665 DOI: 10.3767/persoonia.2023.47.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/12/2021] [Indexed: 02/16/2024]
Abstract
Fungi are rich in complexes of cryptic species that need a combination of different approaches to be delimited, including genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. In this study we present a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana s.lat. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and among three clades in B. bassiana, supporting their subdivision as distinct species. Morphological examination focusing on the width and the length of phialides and conidia showed no difference among the clades within B. bassiana while conidial length was significantly different among clades within B. asiatica. The secondary metabolite profiles obtained by liquid chromatography-mass spectrometry (LC-MS) allowed a distinction between B. asiatica and B. bassiana, but not between the clades therein. Based on these genomic, morphological, chemical data, we proposed a clade of B. asiatica as a new species, named B. thailandica, and two clades of B. bassiana to respectively represent B. namnaoensis and B. neobassiana spp. nov. Such closely related but divergent species with different host ranges have potential to elucidate the evolution of host specificity, with potential biocontrol application. Citation: Kobmoo N, Arnamnart N, Pootakham W, et al. 2021. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia 47: 136-150. https://doi.org/10.3767/persoonia.2021.47.04.
Collapse
Affiliation(s)
- N. Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - N. Arnamnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - W. Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - C. Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - A. Khonsanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - W. Kuephadungphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - R. Suntivich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - O.V. Mosunova
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Giraud
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - J.J. Luangsa-ard
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
30
|
Hayward A, Poulin R, Nakagawa S. A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence. Ecol Lett 2021; 24:1681-1696. [PMID: 33987932 DOI: 10.1111/ele.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/21/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023]
Abstract
Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.
Collapse
Affiliation(s)
- Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
31
|
Bruns EL, Antonovics J, Hood ME. From generalist to specialists: Variation in the host range and performance of anther-smut pathogens on Dianthus. Evolution 2021; 75:2494-2508. [PMID: 33983636 DOI: 10.1111/evo.14264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/05/2021] [Accepted: 04/24/2021] [Indexed: 12/22/2022]
Abstract
Determining the processes that drive the evolution of pathogen host range can inform our understanding of disease dynamics and the potential for host shifts. In natural populations, patterns of host range could be driven by genetically based differences in pathogen infectivity or ecological differences in host availability. In northwestern Italy, four reproductively isolated lineages of the fungal plant-pathogen Microbotryum have been shown to co-occur on several species in the genus Dianthus. We carried out cross-inoculation experiments to determine whether patterns of realized host range in these four lineages were driven by differences in infectivity and to test whether there was evidence of a trade-off between host range and within-host reproduction. We found strong concordance between field patterns of host range and pathogen infectivity on different Dianthus species using experimental inoculation, indicating that infection ability is a major driving force of host range. However, we found no evidence of a trade-off between the ability to infect a wider range of host species and spore production on a shared host.
Collapse
Affiliation(s)
- Emily L Bruns
- Current Address: Department of Biology, University of Maryland, College Park, Maryland, 20742
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002
| |
Collapse
|
32
|
Bundhun D, Jeewon R, Senanayake IC, Erio Camporesi, Aluthmuhandiram JVS, Tang AMC, Ji-Chuan Kang, Bhoyroo V, Hyde KD. Morpho-molecular characterization of Discosia ravennica sp. nov. and a new host record for Sporocadus rosigena. MycoKeys 2021; 79:173-192. [PMID: 33958954 PMCID: PMC8096799 DOI: 10.3897/mycokeys.79.60662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/29/2021] [Indexed: 11/12/2022] Open
Abstract
Collections of fungal samples from two dead leaf specimens from Italy were subjected to morphological examination and phylogenetic analyses. Two coelomycetous taxa belonging to two different genera in Xylariomycetidae, Sordariomycetes, namely Discosia and Sporocadus, were identified. The Discosia taxon is revealed as a new species and is herein introduced as Discosia ravennica sp. nov. while the Sporocadus taxon is identified as Sporocadus rosigena. Multi-locus phylogeny based on DNA sequence data of the large subunit (LSU) and internal transcribed spacer (ITS) of nuclear ribosomal genes, β-tubulin (β-tub) and RNA polymerase II second largest subunit (rpb2) showed that D. ravennica is related to D. neofraxinea but it forms an independent lineage that supports its new species status. The new taxon also differs from other Discosia species by its unilocular to bilocular, superficial and applanate conidiomata with basal stroma composed of cells of textura angularis, elongate-ampulliform conidiogenous cells and conidia smaller in size. Sporocadus rosigena is here reported as a new host record from Quercus ilex from Italy. Descriptions, illustrations and molecular data for both species are provided in this paper.
Collapse
Affiliation(s)
- Digvijayini Bundhun
- Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, Guizhou Province 550025, China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand.,Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
| | - Indunil C Senanayake
- College of Life Science and Oceanography, Shenzhen University, 1068, Nanhai Avenue, Nanshan, Shenzhen, 518055, China.,Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225, China
| | - Erio Camporesi
- A.M.B. Gruppo Micologico Forlivese "Antonio Cicognani", Via Roma, Forli, Italy.,A.M.B. Circolo Micologico "Giovanni Carini", Brescia, Italy.,Società per gli Studi Naturalistici della Romagna, Bagnacavallo (RA), Italy
| | - Janith V S Aluthmuhandiram
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand.,Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Alvin M C Tang
- Division of Applied Science, College of International Education, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ji-Chuan Kang
- Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, Guizhou Province 550025, China
| | | | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand.,Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225, China
| |
Collapse
|
33
|
Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
Collapse
Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| |
Collapse
|
34
|
Fontaine MC, Labbé F, Dussert Y, Delière L, Richart-Cervera S, Giraud T, Delmotte F. Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola. Curr Biol 2021; 31:2155-2166.e4. [PMID: 33770491 DOI: 10.1016/j.cub.2021.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/04/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. We analyzed a comprehensive dataset of ∼2,000 samples, collected from the most important wine-producing countries, using nuclear and mitochondrial gene sequences and microsatellite markers. Population genetic analyses revealed very low genetic diversity in invasive downy mildew populations worldwide and little evidence of admixture. All the invasive populations originated from only one of the five native North American lineages, the one parasitizing wild summer grape (V. aestivalis). An approximate Bayesian computation-random forest approach allowed inferring the worldwide invasion scenario of P. viticola. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa, and twice independently, Australia. Only the invasion of Argentina probably represents a tertiary introduction, from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. Our study will also help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.
Collapse
Affiliation(s)
- Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103 CC, Groningen, the Netherlands; Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France; Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France.
| | - Frédéric Labbé
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103 CC, Groningen, the Netherlands; Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France
| | - Yann Dussert
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Sylvie Richart-Cervera
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France
| | - François Delmotte
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France.
| |
Collapse
|
35
|
Allopatric Plant Pathogen Population Divergence following Disease Emergence. Appl Environ Microbiol 2021; 87:AEM.02095-20. [PMID: 33483307 DOI: 10.1128/aem.02095-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Within the landscape of globally distributed pathogens, populations differentiate via both adaptive and nonadaptive forces. Individual populations are likely to show unique trends of genetic diversity, host-pathogen interaction, and ecological adaptation. In plant pathogens, allopatric divergence may occur particularly rapidly within simplified agricultural monoculture landscapes. As such, the study of plant pathogen populations in monocultures can highlight the distinct evolutionary mechanisms that lead to local genetic differentiation. Xylella fastidiosa is a plant pathogen known to infect and damage multiple monocultures worldwide. One subspecies, Xylella fastidiosa subsp. fastidiosa, was first introduced to the United States ∼150 years ago, where it was found to infect and cause disease in grapevines (Pierce's disease of grapevines, or PD). Here, we studied PD-causing subsp. fastidiosa populations, with an emphasis on those found in the United States. Our study shows that following their establishment in the United States, PD-causing strains likely split into populations on the East and West Coasts. This diversification has occurred via both changes in gene content (gene gain/loss events) and variations in nucleotide sequence (mutation and recombination). In addition, we reinforce the notion that PD-causing populations within the United States acted as the source for subsequent subsp. fastidiosa outbreaks in Europe and Asia.IMPORTANCE Compared to natural environments, the reduced diversity of monoculture agricultural landscapes can lead bacterial plant pathogens to quickly adapt to local biological and ecological conditions. Because of this, accidental introductions of microbial pathogens into naive regions represents a significant economic and environmental threat. Xylella fastidiosa is a plant pathogen with an expanding host and geographic range due to multiple intra- and intercontinental introductions. X. fastidiosa subsp. fastidiosa infects and causes disease in grapevines (Pierce's disease of grapevines [PD]). This study focused on PD-causing X. fastidiosa populations, particularly those found in the United States but also invasions into Taiwan and Spain. The analysis shows that PD-causing X. fastidiosa has diversified via multiple cooccurring evolutionary forces acting at an intra- and interpopulation level. This analysis enables a better understanding of the mechanisms leading to the local adaptation of X. fastidiosa and how a plant pathogen diverges allopatrically after multiple and sequential introduction events.
Collapse
|
36
|
Saadani M, Hönig L, Bien S, Koehler M, Rutten G, Wubet T, Braun U, Bruelheide H. Local Tree Diversity Suppresses Foliar Fungal Infestation and Decreases Morphological But Not Molecular Richness in a Young Subtropical Forest. J Fungi (Basel) 2021; 7:173. [PMID: 33673628 PMCID: PMC7997179 DOI: 10.3390/jof7030173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022] Open
Abstract
Leaf fungal pathogens alter their host species' performance and, thus, changes in fungal species composition can translate into effects at the tree community scale. Conversely, the functional diversity of tree species in a host tree's local neighbourhood can affect the host's foliar fungal infestation. Therefore, understanding the factors that affect fungal infestations is important to advance our understanding of biodiversity-ecosystem functioning (BEF) relationships. Here we make use of the largest BEF tree experiment worldwide, the BEF-China experiment, where we selected tree host species with different neighbour species. Identifying fungal taxa by microscopy and by high-throughput DNA sequencing techniques based on the internal transcribed spacer (ITS) rDNA region, we analysed the fungal richness and infestation rates of our target trees as a function of local species richness. Based on the visual microscopic assessment, we found that a higher tree diversity reduced fungal richness and host-specific fungal infestation in the host's local neighbourhood, while molecular fungal richness was unaffected. This diversity effect was mainly explained by the decrease in host proportion. Thus, the dilution of host species in the local neighbourhood was the primary mechanism in reducing the fungal disease severity. Overall, our study suggests that diverse forests will suffer less from foliar fungal diseases compared to those with lower diversity.
Collapse
Affiliation(s)
- Mariem Saadani
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| | - Lydia Hönig
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Steffen Bien
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Michael Koehler
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Gemma Rutten
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle, Germany
| | - Uwe Braun
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| |
Collapse
|
37
|
Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
Collapse
Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| |
Collapse
|
38
|
Pordel A, Ravel S, Charriat F, Gladieux P, Cros-Arteil S, Milazzo J, Adreit H, Javan-Nikkhah M, Mirzadi-Gohari A, Moumeni A, Tharreau D. Tracing the Origin and Evolutionary History of Pyricularia oryzae Infecting Maize and Barnyard Grass. PHYTOPATHOLOGY 2021; 111:128-136. [PMID: 33100147 DOI: 10.1094/phyto-09-20-0423-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Blast disease is a notorious fungal disease leading to dramatic yield losses on major food crops such as rice and wheat. The causal agent, Pyricularia oryzae, encompasses different lineages, each having a different host range. Host shifts are suspected to have occurred in this species from Setaria spp. to rice and from Lolium spp. to wheat. The emergence of blast disease on maize in Iran was observed for the first time in the north of the country in 2012. We later identified blast disease in two additional regions of Iran: Gilan in 2013 and Golestan in 2016. Epidemics on the weed barnyard grass (Echinochloa spp.) were also observed in the same maize fields. Here, we showed that P. oryzae is the causal agent of this disease on both hosts. Pathogenicity assays in the greenhouse revealed that strains from maize can infect barnyard grass and conversely. However, genotyping with simple sequence repeat markers and comparative genomics showed that strains causing field epidemics on maize and on barnyard grass are different, although they belong to the same previously undescribed clade of P. oryzae. Phylogenetic analyses including these strains and a maize strain collected in Gabon in 1985 revealed two independent host-range expansion events from barnyard grass to maize. Comparative genomics between maize and barnyard grass strains revealed the presence or absence of five candidate genes associated with host specificity on maize, with the deletion of a small genomic region possibly responsible for adaptation to maize. This recent emergence of P. oryzae on maize provides a case study to understand host range expansion. Epidemics on maize raise concerns about potential yield losses on this crop in Iran and potential geographic expansion of the disease.
Collapse
Affiliation(s)
- Adel Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - Sebastien Ravel
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
| | - Florian Charriat
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Pierre Gladieux
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joelle Milazzo
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
| | - Henri Adreit
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
| | - Mohammad Javan-Nikkhah
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Amir Mirzadi-Gohari
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ali Moumeni
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization, Postal-Code46191-91951, Km 8 Babol Rd., Amol, Mazandaran, Iran
| | - Didier Tharreau
- BGPI, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
| |
Collapse
|
39
|
Cook DE, Kramer HM, Torres DE, Seidl MF, Thomma BPHJ. A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen. eLife 2020; 9:e62208. [PMID: 33337321 PMCID: PMC7781603 DOI: 10.7554/elife.62208] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus Verticillium dahliae. We identified incomplete DNA methylation of repetitive elements, associated with specific genomic compartments originally defined as Lineage-Specific (LS) regions that contain genes involved in host adaptation. Further chromatin characterization revealed associations with features such as H3 Lys-27 methylated histones (H3K27me3) and accessible DNA. Machine learning trained on chromatin data identified twice as much LS DNA as previously recognized, which was validated through orthogonal analysis, and we propose to refer to this DNA as adaptive genomic regions. Our results provide evidence that specific chromatin profiles define adaptive genomic regions, and highlight how different epigenetic factors contribute to the organization of these regions.
Collapse
Affiliation(s)
- David E Cook
- Department of Plant Pathology, Kansas State UniversityManhattanUnited States
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
| | - David E Torres
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht UniversityUtrechtNetherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht UniversityUtrechtNetherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| |
Collapse
|
40
|
Zaidi SSEA, Mahas A, Vanderschuren H, Mahfouz MM. Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome Biol 2020; 21:289. [PMID: 33256828 PMCID: PMC7702697 DOI: 10.1186/s13059-020-02204-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/13/2020] [Indexed: 12/19/2022] Open
Abstract
To meet increasing global food demand, breeders and scientists aim to improve the yield and quality of major food crops. Plant diseases threaten food security and are expected to increase because of climate change. CRISPR genome-editing technology opens new opportunities to engineer disease resistance traits. With precise genome engineering and transgene-free applications, CRISPR is expected to resolve the major challenges to crop improvement. Here, we discuss the latest developments in CRISPR technologies for engineering resistance to viruses, bacteria, fungi, and pests. We conclude by highlighting current concerns and gaps in technology, as well as outstanding questions for future research.
Collapse
Affiliation(s)
- Syed Shan-E-Ali Zaidi
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Hervé Vanderschuren
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, Leuven, Belgium
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
41
|
Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Ma WJ, Hood ME, Giraud T. Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence. Mol Biol Evol 2020; 37:668-682. [PMID: 31651949 PMCID: PMC7038665 DOI: 10.1093/molbev/msz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.
Collapse
Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Wen-Juan Ma
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Michael E Hood
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| |
Collapse
|
42
|
Paap T, Wingfield MJ, Burgess TI, Hulbert JM, Santini A. Harmonising the fields of invasion science and forest pathology. NEOBIOTA 2020. [DOI: 10.3897/neobiota.62.52991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Invasive alien species are widely recognised as significant drivers of global environmental change, with far reaching ecological and socio-economic impacts. The trend of continuous increases in first records, with no apparent sign of saturation, is consistent across all taxonomic groups. However, taxonomic biases exist in the extent to which invasion processes have been studied. Invasive forest pathogens have caused, and they continue to result in dramatic damage to natural forests and woody ecosystems, yet their impacts are substantially underrepresented in the invasion science literature. Conversely, most studies of forest pathogens have been undertaken in the absence of a connection to the frameworks developed and used to study biological invasions. We believe this is, in part, a consequence of the mechanistic approach of the discipline of forest pathology; one that has been inherited from the broader discipline of plant pathology. Rather than investigating the origins of, and the processes driving the arrival of invasive microorganisms, the focus of pathologists is generally to investigate specific interactions between hosts and pathogens, with an emphasis on controlling the resulting disease problems. In contrast, central to the field of invasion science, which finds its roots in ecology, is the development and testing of general concepts and frameworks. The lack of knowledge of microbial biodiversity and ecology, speciation and geographic origin present challenges in understanding invasive forest pathogens under existing frameworks, and there is a need to address this shortfall. Advances in molecular technologies such as gene and genome sequencing and metagenomics studies have increased the “visibility” of microorganisms. We consider whether these technologies are being adequately applied to address the gaps between forest pathology and invasion science. We also interrogate the extent to which the two fields stand to gain by becoming more closely linked.
Collapse
|
43
|
Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus Cryphonectria. mSphere 2020; 5:5/5/e00737-20. [PMID: 33055257 PMCID: PMC7565894 DOI: 10.1128/msphere.00737-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic repertoire enabling the colonization and exploitation of host species. Here, we have assembled >100 genomes across two related genera to identify key genomic determinants leading to the emergence of chestnut blight. We found subtle yet highly specific changes in the transition from saprotrophy to latent pathogenicity mostly determined by enzymes involved in carbohydrate metabolism. Large-scale genomic analyses of genes underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens. Emerging fungal pathogens are a threat to forest and agroecosystems, as well as animal and human health. How pathogens evolve from nonpathogenic ancestors is still poorly understood, making the prediction of future outbreaks challenging. Most pathogens have evolved lifestyle adaptations, which were enabled by specific changes in the gene content of the species. Hence, understanding transitions in the functions encoded by genomes gives valuable insight into the evolution of pathogenicity. Here, we studied lifestyle evolution in the genus Cryphonectria, including the prominent invasive pathogen Cryphonectria parasitica, the causal agent of chestnut blight on Castanea species. We assembled and compared the genomes of pathogenic and putatively nonpathogenic Cryphonectria species, as well as sister group pathogens in the family Cryphonectriaceae (Diaporthales, Ascomycetes), to investigate the evolution of genome size and gene content. We found a striking loss of genes associated with carbohydrate metabolism (CAZymes) in C. parasitica compared to other Cryphonectriaceae. Despite substantial CAZyme gene loss, experimental data suggest that C. parasitica has retained wood colonization abilities shared with other Cryphonectria species. Putative effectors substantially varied in number, cysteine content, and protein length among species. In contrast, secondary metabolite gene clusters show a high degree of conservation within the genus. Overall, our results underpin the recent lifestyle transition of C. parasitica toward a more pathogenic lifestyle. Our findings suggest that a CAZyme loss may have promoted pathogenicity of C. parasitica on Castanea species. Analyzing gene complements underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens. IMPORTANCE Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic repertoire enabling the colonization and exploitation of host species. Here, we have assembled >100 genomes across two related genera to identify key genomic determinants leading to the emergence of chestnut blight. We found subtle yet highly specific changes in the transition from saprotrophy to latent pathogenicity mostly determined by enzymes involved in carbohydrate metabolism. Large-scale genomic analyses of genes underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens.
Collapse
|
44
|
Prabhukarthikeyan SR, Parameswaran C, Keerthana U, Teli B, Jag PTK, Cayalvizhi B, Panneerselvam P, Senapati A, Nagendran K, Kumari S, Yadav MK, Aravindan S, Sanghamitra S. Understanding the Plant-microbe Interactions in CRISPR/CAS9 Era: Indeed a Sprinting Start in Marathon. Curr Genomics 2020; 21:429-443. [PMID: 33093805 PMCID: PMC7536795 DOI: 10.2174/1389202921999200716110853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/21/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
Plant-microbe interactions can be either beneficial or harmful depending on the nature of the interaction. Multifaceted benefits of plant-associated microbes in crops are well documented. Specifically, the management of plant diseases using beneficial microbes is considered to be eco-friendly and the best alternative for sustainable agriculture. Diseases caused by various phytopathogens are responsible for a significant reduction in crop yield and cause substantial economic losses globally. In an ecosystem, there is always an equally daunting challenge for the establishment of disease and development of resistance by pathogens and plants, respectively. In particular, comprehending the complete view of the complex biological systems of plant-pathogen interactions, co-evolution and plant growth promotions (PGP) at both genetic and molecular levels requires novel approaches to decipher the function of genes involved in their interaction. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) is a fast, emerging, precise, eco-friendly and efficient tool to address the challenges in agriculture and decipher plant-microbe interaction in crops. Nowadays, the CRISPR/CAS9 approach is receiving major attention in the field of functional genomics and crop improvement. Consequently, the present review updates the prevailing knowledge in the deployment of CRISPR/CAS9 techniques to understand plant-microbe interactions, genes edited for the development of fungal, bacterial and viral disease resistance, to elucidate the nodulation processes, plant growth promotion, and future implications in agriculture. Further, CRISPR/CAS9 would be a new tool for the management of plant diseases and increasing productivity for climate resilience farming.
Collapse
Affiliation(s)
| | | | - Umapathy Keerthana
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Basavaraj Teli
- Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | | | | | - Periyasamy Panneerselvam
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Ansuman Senapati
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Krishnan Nagendran
- Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, Uttar Pradesh, India
| | - Shweta Kumari
- Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, Uttar Pradesh, India
| | - Manoj Kumar Yadav
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Sundaram Aravindan
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| | - Samantaray Sanghamitra
- Crop Improvement Division, National Rice Research Institute (ICAR-NRRI), Cuttack, 753006 Odisha, India
| |
Collapse
|
45
|
Ahmar S, Saeed S, Khan MHU, Ullah Khan S, Mora-Poblete F, Kamran M, Faheem A, Maqsood A, Rauf M, Saleem S, Hong WJ, Jung KH. A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement. Int J Mol Sci 2020; 21:E5665. [PMID: 32784649 PMCID: PMC7461041 DOI: 10.3390/ijms21165665] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist's mind, as it allows genome editing in multiple biological systems.
Collapse
Affiliation(s)
- Sunny Ahmar
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Sumbul Saeed
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Muhammad Hafeez Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Shahid Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Muhammad Kamran
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
| | - Aroosha Faheem
- Sate Key Laboratory of Agricultural Microbiology and State Key Laboratory of Microbial Biosensor, College of Life Sciences Huazhong Agriculture University Wuhan, Wuhan 430070, China;
| | - Ambreen Maqsood
- Department of Plant Pathology, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Muhammad Rauf
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan;
| | - Saba Saleem
- Department of Bioscience, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan;
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
| |
Collapse
|
46
|
Dar MS, Padder BA, Ahmad M, Sofi TA, Mir AA, Nabi A, Shah MD. Population structure of Venturia inaequalis, a hemibiotrophic fungus, under different host resistance specificities in the Kashmir valley. Arch Microbiol 2020; 202:2245-2253. [PMID: 32533207 DOI: 10.1007/s00203-020-01950-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/25/2022]
Abstract
Venturia inaequalis is a notorious fungal pathogen and show classical gene for gene interaction with its apple host. Neutral markers provide clues about history, evolutionary potential, genetic diversity and population structure of V. inaequalis. The genetic diversity and population structure of fungus indicates that the pathogen is highly diverse with the capacity to breach the scab resistance genes. In the present study, we collected 108 V. inaequalis isolates from three apple cultivars differing in Rvi1 resistance gene. Based on the AMOVA, the variation was mostly distributed among the isolates, providing evidence of non-existence of subpopulation in orchards thus founder population is difficult to arise in Kashmir apple orchards. Pair wise genetic differentiation is less due to regular occurrence of gene flow between the populations residing on different orchard as infected material is transported without stringent quarantine measures. Based on principal coordinate analysis and clustering algorithm as implemented in STRUCTURE, we observed admixture between the two subpopulations, which is quite low, suggesting the existence of pre-zygotic and post-zygotic barriers to gene flow and we cannot rule out the existence of other structures shared by accessions belonging to different varieties. Due to the continuous increase in introduction and monoculture of apple varieties, mixed orchard with different host resistance specificities are more suitable for managing the apple scab in Kashmir valley.
Collapse
Affiliation(s)
- M S Dar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
| | - Mushtaq Ahmad
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - T A Sofi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - A A Mir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Asha Nabi
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-K, Sopore, Wadura, 193201, India
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| |
Collapse
|
47
|
Thibert-Plante X, Præbel K, Østbye K, Kahilainen KK, Amundsen PA, Gavrilets S. Using mathematical modelling to investigate the adaptive divergence of whitefish in Fennoscandia. Sci Rep 2020; 10:7394. [PMID: 32355195 PMCID: PMC7193591 DOI: 10.1038/s41598-020-63684-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023] Open
Abstract
Modern speciation theory has greatly benefited from a variety of simple mathematical models focusing on the conditions and patterns of speciation and diversification in the presence of gene flow. Unfortunately the application of general theoretical concepts and tools to specific ecological systems remains a challenge. Here we apply modeling tools to better understand adaptive divergence of whitefish during the postglacial period in lakes of northern Fennoscandia. These lakes harbor up to three different morphs associated with the three major lake habitats: littoral, pelagic, and profundal. Using large-scale individual-based simulations, we aim to identify factors required for in situ emergence of the pelagic and profundal morphs in lakes initially colonized by the littoral morph. The importance of some of the factors we identify and study - sufficiently large levels of initial genetic variation, size- and habitat-specific mating, sufficiently large carrying capacity of the new niche - is already well recognized. In addition, our model also points to two other factors that have been largely disregarded in theoretical studies: fitness-dependent dispersal and strong predation in the ancestral niche coupled with the lack of it in the new niche(s). We use our theoretical results to speculate about the process of diversification of whitefish in Fennoscandia and to identify potentially profitable directions for future empirical research.
Collapse
Affiliation(s)
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Kjartan Østbye
- Inland Norway University of Applied Sciences, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad, Anne Evenstadsvei 80, NO-2480, Koppang, Norway.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Kimmo K Kahilainen
- Lammi Biological Station, University of Helsinki, Pääjärventie 320, FI-16900, Lammi, Finland
| | - Per-Arne Amundsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sergey Gavrilets
- Department of Ecology and Evolutionary Biology, Department of Mathematics, National Institute for Mathematical and Biological Synthesis (NIMBioS), Center for the Dynamics of Social Complexity (DySoC), University of Tennessee, Knoxville, TN, 37996, USA
| |
Collapse
|
48
|
Cabral A, Azinheira HG, Talhinhas P, Batista D, Ramos AP, Silva MDC, Oliveira H, Várzea V. Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E502. [PMID: 32295225 PMCID: PMC7238176 DOI: 10.3390/plants9040502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/20/2022]
Abstract
The genus Colletotrichum has witnessed tremendous variations over the years in the number of species recognized, ranging from 11 to several hundreds. Host-specific fungal species, once the rule, are now the exception, with polyphagous behavior regarded as normal in this genus. The species Colletotrichum kahawae was created to accommodate the pathogens that have the unique ability to infect green developing coffee berries causing the devastating Coffee Berry Disease in Africa, but its close phylogenetic relationship to a polyphagous group of fungi in the C. gloeosporioides species complex led some researchers to regard these pathogens as members of a wider species. In this work we combine pathological, morphological, cytogenomic, biochemical, and molecular data of a comprehensive set of phylogenetically-related isolates to show that the Coffee Berry Disease pathogen forms a separate species, C. kahawae, and also to assign the closely related fungi, previously in C. kahawae subsp. cigarro, to a new species, C. cigarro comb. et stat. nov. This taxonomic clarification provides an opportunity to link phylogeny and functional biology, and additionally enables a much-needed tool for plant pathology and agronomy, associating exclusively C. kahawae to the Coffee Berry Disease pathogen.
Collapse
Affiliation(s)
- Ana Cabral
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Helena G. Azinheira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Dora Batista
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Ana Paula Ramos
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Laboratório de Patologia Vegetal “Veríssimo de Almeida”, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Maria do Céu Silva
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Helena Oliveira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
| | - Vítor Várzea
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| |
Collapse
|
49
|
Wang Q, Sun M, Zhang Y, Song Z, Zhang S, Zhang Q, Xu J, Liu H. Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi. MOLECULAR PLANT PATHOLOGY 2020; 21:330-348. [PMID: 31916390 PMCID: PMC7036362 DOI: 10.1111/mpp.12899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/06/2019] [Accepted: 11/28/2019] [Indexed: 05/11/2023]
Abstract
The basal ascomycetes in genus Taphrina have strict host specificity and coevolution with their host plants, making them appealing models for studying the genomic basis of ecological divergence and host adaption. We therefore performed genome sequencing and comparative genomics of different Taphrina species with distinct host ranges to reveal their evolution. We identified frequent chromosomal rearrangements and highly dynamic lineage-specific (LS) genomic regions in Taphrina genomes. The LS regions occur at the flanking regions of chromosomal breakpoints, and are greatly enriched for DNA repeats, non-core genes, and in planta up-regulated genes. Furthermore, we identified hundreds of candidate secreted effector proteins (CSEPs) that are commonly organized in gene clusters that form distinct AT-rich isochore-like regions. Nearly half of the CSEPs constitute two novel superfamilies with modular structures unique to Taphrina. These CSEPs are commonly up-regulated during infection, enriched in the LS regions, evolved faster, and underwent extensive gene gain and loss in different species. In addition to displaying signatures of positive selection, functional characterization of selected CSEP genes confirmed their roles in suppression of plant defence responses. Overall, our results showed that extensive chromosomal rearrangements and rapidly evolving CSEP superfamilies play important roles in speciation and host adaptation in the early-branching ascomycetous fungi.
Collapse
Affiliation(s)
- Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yimei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Zhenzhen Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Qiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jin‐Rong Xu
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| |
Collapse
|
50
|
Tabima JF, Søndreli KL, Keriö S, Feau N, Sakalidis ML, Hamelin RC, LeBoldus JM. Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:189-199. [PMID: 31593527 DOI: 10.1094/mpmi-05-19-0131-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.
Collapse
Affiliation(s)
- J F Tabima
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
| | - K L Søndreli
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
| | - S Keriö
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
| | - N Feau
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Canada
| | - M L Sakalidis
- Department of Plant, Soil and Microbial Sciences and the Department of Forestry, College of Agriculture & Natural Resources, Michigan State University, East Lansing, U.S.A
| | - R C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Canada
| | - J M LeBoldus
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
- Department of Forest Engineering, Resources and Management, College of Forestry, Oregon State University
| |
Collapse
|