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Ulrich L, Steiner LX, Giez C, Lachnit T. Optimizing bacteriophage treatment of resistant Pseudomonas. mSphere 2024; 9:e0070723. [PMID: 38934592 PMCID: PMC11288017 DOI: 10.1128/msphere.00707-23] [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: 11/16/2023] [Accepted: 04/15/2024] [Indexed: 06/28/2024] Open
Abstract
Phage therapy is increasing in relevance as an alternative treatment to combat antibiotic resistant bacteria. Phage cocktails are the state-of-the-art method of administering phages in clinical settings, preferred over monophage treatment because of their ability to eliminate multiple bacterial strains and reduce resistance formation. In our study, we compare monophage applications and phage cocktails to our chosen method of phage sequential treatments. To do so, we isolated four novel bacteriophages capable of infecting Pseudomonas alcaligenes T3, a close relative of P. aeruginosa, and characterized them using sequencing and transmission electron microscopy. While investigating monophage treatments, we observed that different phage concentrations had a strong impact on the timing and amount of resistance formation. When using phage cocktails, we observed that P. alcaligenes were capable of forming resistance in the same timespan it took them to become resistant to single phages. We isolated mutants resistant to each single phage as well as mutants exposed to phage cocktails, resulting in bacteria resistant to all four phages at once. Sequencing these mutants showed that different treatments yielded unique single nucleotide polymorphism mutation patterns. In order to combat resistance formation, we added phages one by one in intervals of 24 h, thus managing to delay resistance development and keeping bacterial growth significantly lower compared to phage cocktails.IMPORTANCEWHO declared antimicrobial resistance a top threat to global health; while antibiotics have stood at the forefront in the fight against bacterial infection, the increasing number of multidrug-resistant bacteria highlights a need to branch out in order to address the threat of antimicrobial resistance. Bacteriophages, viruses solely infecting bacteria, could present a solution due to their abundance, versatility, and adaptability. For this study, we isolated new phages infecting a fast-mutating Pseudomonas alcaligenes strain capable of forming resistance within 30 h. By using a sequential treatment approach of adding one phage after another, we were able to curb bacterial growth significantly more compared to state-of-the-art phage cocktails.
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Affiliation(s)
- Laura Ulrich
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Leon X. Steiner
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Christoph Giez
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts Universität zu Kiel, Kiel, Germany
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2
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Rogério F, Baroncelli R, Cuevas-Fernández FB, Becerra S, Crouch J, Bettiol W, Azcárate-Peril MA, Malapi-Wight M, Ortega V, Betran J, Tenuta A, Dambolena JS, Esker PD, Revilla P, Jackson-Ziems TA, Hiltbrunner J, Munkvold G, Buhiniček I, Vicente-Villardón JL, Sukno SA, Thon MR. Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose. mBio 2023; 14:e0287822. [PMID: 36533926 PMCID: PMC9973043 DOI: 10.1128/mbio.02878-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.
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Affiliation(s)
- Flávia Rogério
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Riccardo Baroncelli
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Francisco Borja Cuevas-Fernández
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sioly Becerra
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - JoAnne Crouch
- Foreign Disease and Weed Science Unit, United States Department of Agriculture, Fort Detrick, Maryland, USA
| | | | - M. Andrea Azcárate-Peril
- Center for Gastrointestinal Biology and Disease, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Martha Malapi-Wight
- USDA Animal and Plant Health Inspection Services, Biotechnology Regulatory Services, Riverdale, Maryland, USA
| | | | | | - Albert Tenuta
- Ontario Ministry of Agriculture, Food, and Rural Affairs, University of Guelph-Ridgetown, Ridgetown, Ontario, Canada
| | - José S. Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, IMBIV-CONICET-ICTA, Córdoba, Argentina
| | - Paul D. Esker
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Pedro Revilla
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Pontevedra, Spain
| | | | | | - Gary Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ivica Buhiniček
- BC Institute for Breeding and Production of Field Crops, Dugo Selo, Croatia
| | | | - Serenella A. Sukno
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Michael R. Thon
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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3
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Belisário R, Robertson AE, Vaillancourt LJ. Maize Anthracnose Stalk Rot in the Genomic Era. PLANT DISEASE 2022; 106:2281-2298. [PMID: 35291814 DOI: 10.1094/pdis-10-21-2147-fe] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Anthracnose stalk rot (ASR) of maize results in millions of dollars in losses annually in the United States. ASR, together with anthracnose leaf blight and anthracnose top dieback, is caused by the fungus Colletotrichum graminicola. Current ASR management recommendations emphasize host resistance and reduction of plant stressors (e.g., drought, heat, low fertility, or soil acidity). Stress reduction may be more difficult to achieve in the future due to more high-intensity production protocols and climate change. Moreover, cultural and chemical management practices may conflict with other important goals, including environmental sustainability and maximization of yield potential. Thus, future ASR management may rely more heavily on host resistance, for which there are relatively few highly effective sources. The last comprehensive review of C. graminicola and maize anthracnose was written over two decades ago. The genomic age has brought important new insights into mechanisms governing the host-pathogen interaction from the application of molecular and cytological technologies. This review provides a summary of our current model of maize anthracnose etiology, including how increased knowledge of molecular and cellular events could contribute to better ASR management. Improved understanding of C. graminicola taxonomy has confirmed that the fungus is specific to Zea mays, and that it colonizes living maize tissues via a critical biotrophic phase. Successful biotrophic establishment relies on an array of secreted protein effectors and secondary metabolites produced at different stages of infection and dispersed to multiple locations. These molecules could provide therapeutic targets for the next generation of transgenic or gene-edited ASR-resistant hybrids.
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Affiliation(s)
- Renata Belisário
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY 40546-0312
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, 1344 Advanced Teaching and Research Building, 2213 Pammel Drive, Ames, IA 50011
| | - Lisa J Vaillancourt
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY 40546-0312
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4
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Lu X, Miao J, Shen D, Dou D. Proteinaceous Effector Discovery and Characterization in Plant Pathogenic Colletotrichum Fungi. Front Microbiol 2022; 13:914035. [PMID: 35694285 PMCID: PMC9184758 DOI: 10.3389/fmicb.2022.914035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
Anthracnose caused by plant pathogenic Colletotrichum fungi results in large economic losses in field crop production worldwide. To aid the establishment of plant host infection, Colletotrichum pathogens secrete numerous effector proteins either in apoplastic space or inside of host cells for effective colonization. Understanding these effector repertoires is critical for developing new strategies for resistance breeding and disease management. With the advance of genomics and bioinformatics tools, a large repertoire of putative effectors has been identified in Colletotrichum genomes, and the biological functions and molecular mechanisms of some studied effectors have been summarized. Here, we review recent advances in genomic identification, understanding of evolutional characteristics, transcriptional profiling, and functional characterization of Colletotrichum effectors. We also offer a perspective on future research.
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Affiliation(s)
- Xinyu Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jinlu Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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5
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de Oliveira Silva A, Aliyeva-Schnorr L, Wirsel SGR, Deising HB. Fungal Pathogenesis-Related Cell Wall Biogenesis, with Emphasis on the Maize Anthracnose Fungus Colletotrichum graminicola. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070849. [PMID: 35406829 PMCID: PMC9003368 DOI: 10.3390/plants11070849] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 05/25/2023]
Abstract
The genus Colletotrichum harbors many plant pathogenic species, several of which cause significant yield losses in the field and post harvest. Typically, in order to infect their host plants, spores germinate, differentiate a pressurized infection cell, and display a hemibiotrophic lifestyle after plant invasion. Several factors required for virulence or pathogenicity have been identified in different Colletotrichum species, and adaptation of cell wall biogenesis to distinct stages of pathogenesis has been identified as a major pre-requisite for the establishment of a compatible parasitic fungus-plant interaction. Here, we highlight aspects of fungal cell wall biogenesis during plant infection, with emphasis on the maize leaf anthracnose and stalk rot fungus, Colletotrichum graminicola.
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6
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Wu Q, Wang Y, Liu LN, Shi K, Li CY. Comparative Genomics and Gene Pool Analysis Reveal the Decrease of Genome Diversity and Gene Number in Rice Blast Fungi by Stable Adaption with Rice. J Fungi (Basel) 2021; 8:jof8010005. [PMID: 35049945 PMCID: PMC8778285 DOI: 10.3390/jof8010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Magnaporthe oryzae caused huge losses in rice and wheat production worldwide. Comparing to long-term co-evolution history with rice, wheat-infecting isolates were new-emerging. To reveal the genetic differences between rice and wheat blast on global genomic scale, 109 whole-genome sequences of M. oryzae from rice, wheat, and other hosts were reanalyzed in this study. We found that the rice lineage had gone through stronger selective sweep and fewer conserved genes than those of Triticum and Lolium lineages, which indicated that rice blast fungi adapted to rice by gene loss and rapid evolution of specific loci. Furthermore, 228 genes associated with host adaptation of M. oryzae were found by presence/absence variation (PAV) analyses. The functional annotation of these genes found that the fine turning of genes gain/loss involved with transport and transcription factor, thiol metabolism, and nucleotide metabolism respectively are major mechanisms for rice adaption. This result implies that genetic base of specific host plant may lead to gene gain/loss variation of pathogens, so as to enhance their adaptability to host. Further characterization of these specific loci and their roles in adaption and evaluation of the fungi may eventually lead to understanding of interaction mechanism and develop new strategies of the disease management.
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Affiliation(s)
- Qi Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- College of Science, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
| | - Li-Na Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650201, China
| | - Kai Shi
- School of Foreign Language, Yunnan Agricultural University, Kunming 650201, China;
| | - Cheng-Yun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Correspondence:
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7
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Yuan Z, Druzhinina IS, Gibbons JG, Zhong Z, Van de Peer Y, Rodriguez RJ, Liu Z, Wang X, Wei H, Wu Q, Wang J, Shi G, Cai F, Peng L, Martin FM. Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus. THE ISME JOURNAL 2021; 15:3468-3479. [PMID: 34108667 PMCID: PMC8629976 DOI: 10.1038/s41396-021-01023-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/09/2021] [Accepted: 05/24/2021] [Indexed: 02/05/2023]
Abstract
Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila-S. salsa symbiosis.
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Affiliation(s)
- Zhilin Yuan
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China ,grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Irina S. Druzhinina
- grid.27871.3b0000 0000 9750 7019Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - John G. Gibbons
- grid.266683.f0000 0001 2166 5835Department of Food Science, University of Massachusetts, Amherst, MA USA
| | - Zhenhui Zhong
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China ,grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA USA
| | - Yves Van de Peer
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,grid.511033.5VIB Center for Plant Systems Biology, Ghent, Belgium ,grid.49697.350000 0001 2107 2298Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Russell J. Rodriguez
- grid.34477.330000000122986657Adaptive Symbiotic Technologies, University of Washington, Seattle, WA USA
| | - Zhongjian Liu
- grid.256111.00000 0004 1760 2876Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyu Wang
- grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Huanshen Wei
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China ,grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Qi Wu
- grid.9227.e0000000119573309State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jieyu Wang
- grid.9227.e0000000119573309Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guohui Shi
- grid.9227.e0000000119573309State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng Cai
- grid.27871.3b0000 0000 9750 7019Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Long Peng
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China ,grid.216566.00000 0001 2104 9346Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Francis M. Martin
- grid.66741.320000 0001 1456 856XBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China ,grid.29172.3f0000 0001 2194 6418Université de Lorraine, INRAE, UMR Interactions Arbres/Micro-Organismes, Centre INRAE Grand Est Nancy, Champenoux, France
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Pang R, Xing K, Yuan L, Liang Z, Chen M, Yue X, Dong Y, Ling Y, He X, Li X, Zhang W. Peroxiredoxin alleviates the fitness costs of imidacloprid resistance in an insect pest of rice. PLoS Biol 2021; 19:e3001190. [PMID: 33844686 PMCID: PMC8062100 DOI: 10.1371/journal.pbio.3001190] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 04/22/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Chemical insecticides have been heavily employed as the most effective measure for control of agricultural and medical pests, but evolution of resistance by pests threatens the sustainability of this approach. Resistance-conferring mutations sometimes impose fitness costs, which may drive subsequent evolution of compensatory modifier mutations alleviating the costs of resistance. However, how modifier mutations evolve and function to overcome the fitness cost of resistance still remains unknown. Here we show that overexpression of P450s not only confers imidacloprid resistance in the brown planthopper, Nilaparvata lugens, the most voracious pest of rice, but also leads to elevated production of reactive oxygen species (ROS) through metabolism of imidacloprid and host plant compounds. The inevitable production of ROS incurs a fitness cost to the pest, which drives the increase or fixation of the compensatory modifier allele T65549 within the promoter region of N. lugens peroxiredoxin (NlPrx) in the pest populations. T65549 allele in turn upregulates the expression of NlPrx and thus increases resistant individuals' ability to clear the cost-incurring ROS of any source. The frequent involvement of P450s in insecticide resistance and their capacity to produce ROS while metabolizing their substrates suggest that peroxiredoxin or other ROS-scavenging genes may be among the common modifier genes for alleviating the fitness cost of insecticide resistance.
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Affiliation(s)
- Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Science, Guangzhou, Guangdong, China
| | - Ke Xing
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Longyu Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhikun Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Meng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiangzhao Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi Dong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yan Ling
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (XL); (WZ)
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (XL); (WZ)
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Abstract
Mosaicism refers to the occurrence of two or more genomes in an individual derived from a single zygote. Germline mosaicism is a mutation that is limited to the gonads and can be transmitted to offspring. Somatic mosaicism is a postzygotic mutation that occurs in the soma, and it may occur at any developmental stage or in adult tissues. Mosaic variation may be classified in six ways: (a) germline or somatic origin, (b) class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (c) developmental context, (d) body location(s), (e) functional consequence (including deleterious, neutral, or advantageous), and (f) additional sources of mosaicism, including mitochondrial heteroplasmy, exogenous DNA sources such as vectors, and epigenetic changes such as imprinting and X-chromosome inactivation. Technological advances, including single-cell and other next-generation sequencing, have facilitated improved sensitivity and specificity to detect mosaicism in a variety of biological contexts.
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Affiliation(s)
- Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
| | - Ikeoluwa A Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | | | - Rossella Tupler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA; .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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10
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Atkinson EG, Audesse AJ, Palacios JA, Bobo DM, Webb AE, Ramachandran S, Henn BM. No Evidence for Recent Selection at FOXP2 among Diverse Human Populations. Cell 2018; 174:1424-1435.e15. [PMID: 30078708 DOI: 10.1016/j.cell.2018.06.048] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/15/2018] [Accepted: 06/26/2018] [Indexed: 12/18/2022]
Abstract
FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.
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Affiliation(s)
| | - Amanda Jane Audesse
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA
| | - Julia Adela Palacios
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA; Department of Statistics and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Dean Michael Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Ashley Elizabeth Webb
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Brenna Mariah Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA; Department of Anthropology and the Genome Center, University of California, Davis, Davis, CA 95616, USA.
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11
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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12
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Bronstein O, Kroh A, Haring E. Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids. BMC Evol Biol 2018; 18:80. [PMID: 29848319 PMCID: PMC5977486 DOI: 10.1186/s12862-018-1198-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region. RESULTS Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids. CONCLUSIONS Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.
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Affiliation(s)
- Omri Bronstein
- Natural History Museum Vienna, Geological-Palaeontological Department, 1010 Vienna, Austria
- Natural History Museum Vienna, Central Research Laboratories, 1010 Vienna, Austria
| | - Andreas Kroh
- Natural History Museum Vienna, Geological-Palaeontological Department, 1010 Vienna, Austria
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research Laboratories, 1010 Vienna, Austria
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
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13
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Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum. Proc Natl Acad Sci U S A 2018; 115:E5459-E5466. [PMID: 29844193 PMCID: PMC6004482 DOI: 10.1073/pnas.1712798115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species in the fungal genus Cercospora cause diseases in many important crops worldwide. Their success as pathogens is largely due to the secretion of cercosporin during infection. We report that the cercosporin toxin biosynthesis (CTB) gene cluster is ancient and was horizontally transferred to diverse fungal plant pathogens. Because our analyses revealed genes adjacent to the established CTB cluster with similar evolutionary trajectories, we evaluated their role in Cercospora beticola to show that four are necessary for cercosporin biosynthesis. Lastly, we confirmed that the apple pathogen Colletotrichum fioriniae produces cercosporin, the first case outside the family Mycosphaerellaceae. Other Colletotrichum plant pathogens also harbor the CTB cluster, which points to a wider role that this toxin may play in virulence. Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean, and other major food crops. Here, we sequenced the genome of the sugar beet pathogen Cercospora beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide-host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to rely on an eight-gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein, previously shown to be involved with cercosporin autoresistance, and four additional genes required for cercosporin biosynthesis, including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Lastly, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.
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14
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Zeng Z, Sun H, Vainio EJ, Raffaello T, Kovalchuk A, Morin E, Duplessis S, Asiegbu FO. Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors. BMC Genomics 2018; 19:220. [PMID: 29580224 PMCID: PMC5870257 DOI: 10.1186/s12864-018-4610-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species. RESULTS To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates. CONCLUSION Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence.
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Affiliation(s)
- Zhen Zeng
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Hui Sun
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Eeva J. Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Emmanuelle Morin
- INRA UMR 1136 Interactions Arbres Micro-organismes, INRA Centre Grand Est Nancy, Champenoux, France
| | - Sébastien Duplessis
- INRA UMR 1136 Interactions Arbres Micro-organismes, INRA Centre Grand Est Nancy, Champenoux, France
- UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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15
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Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG. Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC). BMC Genomics 2018; 19:58. [PMID: 29343217 PMCID: PMC5773145 DOI: 10.1186/s12864-018-4440-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. RESULTS We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. CONCLUSION Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity.
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Affiliation(s)
- Eddy Patricia Lopez Molano
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Odalys García Cabrera
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Juliana Jose
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Marcelo Falsarella Carazzolle
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo José Pereira Lima Teixeira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Present Address: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Javier Correa Alvarez
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellın, Colombia
| | - Ricardo Augusto Tiburcio
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Paulo Massanari Tokimatu Filho
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Gustavo Machado Alvares de Lima
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael Victório Carvalho Guido
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Gonçalo Amarante Guimarães Pereira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.
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16
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Panda A, Sen D, Ghosh A, Gupta A, C. MM, Prakash Mishra G, Singh D, Ye W, Tyler BM, Tripathy S. EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes. MOLECULAR PLANT PATHOLOGY 2018; 19:227-237. [PMID: 27785876 PMCID: PMC6638084 DOI: 10.1111/mpp.12505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/09/2016] [Accepted: 10/22/2016] [Indexed: 05/13/2023]
Abstract
We have developed EumicrobeDBLite-a lightweight comprehensive genome resource and sequence analysis platform for oomycete organisms. EumicrobeDBLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, GUS has been greatly simplified with the removal of many obsolete modules and the redesign of others to incorporate contemporary data. Several dependences, such as perl object layers used for data loading in VMD, have been replaced with independent lightweight scripts. EumicrobeDBLite now runs on a powerful annotation engine developed at our laboratory, called 'Genome Annotator Lite'. Currently, this database has 26 publicly available genomes and 10 expressed sequence tag (EST) datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44 777 core conserved proteins from 12 oomycete organisms which form 2974 clusters. Synteny viewing is enabled by the incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every 6 months to ensure quality. The database resource is available at www.eumicrobedb.org.
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Affiliation(s)
- Arijit Panda
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Diya Sen
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Arup Ghosh
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Akash Gupta
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Mathu Malar C.
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Gyan Prakash Mishra
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Deeksha Singh
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
| | - Wenwu Ye
- Center for Genome Research and Biocomputing and Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331‐7303, USA
- Department of Plant PathologyNanjing Agricultural UniversityNanjing210095China
| | - Brett M. Tyler
- Center for Genome Research and Biocomputing and Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331‐7303, USA
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Structural Biology and Bioinformatics DivisionCouncil of Scientific and Industrial Research –Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, JadavpurKolkata700032India
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17
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Buiate EAS, Xavier KV, Moore N, Torres MF, Farman ML, Schardl CL, Vaillancourt LJ. A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics 2017; 18:67. [PMID: 28073340 PMCID: PMC5225507 DOI: 10.1186/s12864-016-3457-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/22/2016] [Indexed: 01/10/2023] Open
Abstract
Background Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. Results Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. Conclusions Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E A S Buiate
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Monsanto Company Brazil, Uberlândia, Minas Gerais, Brazil
| | - K V Xavier
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - N Moore
- Department of Computer Science, University of Kentucky, Davis Marksbury Building, 328 Rose Street, Lexington, KY, 40504-0633, USA
| | - M F Torres
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Functional Genomics Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - M L Farman
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - C L Schardl
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - L J Vaillancourt
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.
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18
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Drinan DP, Galindo HM, Loher T, Hauser L. Subtle genetic population structure in Pacific halibut Hippoglossus stenolepis. JOURNAL OF FISH BIOLOGY 2016; 89:2571-2594. [PMID: 27714808 DOI: 10.1111/jfb.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Pacific halibut Hippoglossus stenolepis from 10 sampling locations throughout their range were investigated for signs of population structure. Two genetic data sets were created: (1) all individuals (n = 828) at few anonymous microsatellite markers (number of loci = 16); (2) fewer individuals (n = 435) genotyped at anonymous as well as expressed sequence-tag linked microsatellites (number of loci = 61). A combination of multidimensional scaling plots, discriminant analysis of principal components and pairwise differentiation estimates suggested that samples from the Aleutian Islands, particularly the western Aleutian Islands, were genetically distinct from samples collected in other regions. In addition, outlier analyses found that two markers linked to expressed sequence tags may be under directional selection and could explain the differentiation among samples. These results confirm findings from previous research and suggest that population structure may exist within a current management unit (i.e. International Pacific Halibut Commission Regulatory Area 4B).
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Affiliation(s)
- D P Drinan
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, U.S.A
| | - H M Galindo
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, U.S.A
| | - T Loher
- International Pacific Halibut Commission, 2320 West Commodore Way, Suite 300, Seattle, WA, 98199, U.S.A
| | - L Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, U.S.A
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19
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Ye W, Wang Y, Tyler BM, Wang Y. Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection. Front Microbiol 2016; 7:1547. [PMID: 27746768 PMCID: PMC5042962 DOI: 10.3389/fmicb.2016.01547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens.
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Affiliation(s)
- Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University Nanjing, China
| | - Yang Wang
- Department of Plant Pathology, Nanjing Agricultural University Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis OR, USA
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University Nanjing, China
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20
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Sanz-Martín JM, Pacheco-Arjona JR, Bello-Rico V, Vargas WA, Monod M, Díaz-Mínguez JM, Thon MR, Sukno SA. A highly conserved metalloprotease effector enhances virulence in the maize anthracnose fungus Colletotrichum graminicola. MOLECULAR PLANT PATHOLOGY 2016; 17:1048-62. [PMID: 26619206 PMCID: PMC6638349 DOI: 10.1111/mpp.12347] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 05/22/2023]
Abstract
Colletotrichum graminicola causes maize anthracnose, an agronomically important disease with a worldwide distribution. We have identified a fungalysin metalloprotease (Cgfl) with a role in virulence. Transcriptional profiling experiments and live cell imaging show that Cgfl is specifically expressed during the biotrophic stage of infection. To determine whether Cgfl has a role in virulence, we obtained null mutants lacking Cgfl and performed pathogenicity and live microscopy assays. The appressorium morphology of the null mutants is normal, but they exhibit delayed development during the infection process on maize leaves and roots, showing that Cgfl has a role in virulence. In vitro chitinase activity assays of leaves infected with wild-type and null mutant strains show that, in the absence of Cgfl, maize leaves exhibit increased chitinase activity. Phylogenetic analyses show that Cgfl is highly conserved in fungi. Similarity searches, phylogenetic analysis and transcriptional profiling show that C. graminicola encodes two LysM domain-containing homologues of Ecp6, suggesting that this fungus employs both Cgfl-mediated and LysM protein-mediated strategies to control chitin signalling.
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Affiliation(s)
- José M Sanz-Martín
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
| | - José Ramón Pacheco-Arjona
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
| | - Víctor Bello-Rico
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
| | - Walter A Vargas
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
| | - Michel Monod
- Laboratoire de Mycologie, Service de Dermatologie, Centre Hospitalier Universitaire Vaudois, 1011, Lausanne, Switzerland
| | - José M Díaz-Mínguez
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
| | - Michael R Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
| | - Serenella A Sukno
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, 37185, Villamayor, Spain
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21
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Malapi-Wight M, Salgado-Salazar C, Demers JE, Clement DL, Rane KK, Crouch JA. Sarcococca Blight: Use of Whole-Genome Sequencing for Fungal Plant Disease Diagnosis. PLANT DISEASE 2016; 100:1093-1100. [PMID: 30682271 DOI: 10.1094/pdis-10-15-1159-re] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effective mitigation strategies and appropriate regulatory responses. Most commonly, pathogen identification relies on morphology and DNA marker analysis. However, for new diseases, these approaches may not be sufficient for precise diagnosis. In this study, we used whole-genome sequencing (WGS) to identify the causal agent of a new disease affecting Sarcococca hookeriana (sarcococca). Blight symptoms were observed on sarcococca and adjacent Buxus sempervirens (boxwood) plants in Maryland during 2014. Symptoms on sarcococca were novel, and included twig dieback and dark lesions on leaves and stems. A Calonectria sp. was isolated from both hosts and used to fulfill Koch's postulates but morphology and marker sequence data precluded species-level identification. A 51.4-Mb WGS was generated for the two isolates and identified both as Calonectria pseudonaviculata. A single-nucleotide polymorphism at a noncoding site differentiated between the two host isolates. These results indicate that the same C. pseudonaviculata genotype has the ability to induce disease on both plant species. This study marks the first application of WGS for fungal plant pathogen diagnosis and demonstrates the power of this approach to rapidly identify causal agents of new diseases.
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Affiliation(s)
- Martha Malapi-Wight
- United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705
| | - Catalina Salgado-Salazar
- USDA-ARS, Systematic Mycology and Microbiology Laboratory; and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08906
| | - Jill E Demers
- USDA-ARS, Systematic Mycology and Microbiology Laboratory
| | - David L Clement
- University of Maryland Home and Garden Information Center, Ellicott City, MD 21042
| | - Karen K Rane
- Plant Diagnostic Laboratory, University of Maryland, College Park 20742
| | - Jo Anne Crouch
- USDA-ARS, Systematic Mycology and Microbiology Laboratory
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22
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Gan P, Narusaka M, Kumakura N, Tsushima A, Takano Y, Narusaka Y, Shirasu K. Genus-Wide Comparative Genome Analyses of Colletotrichum Species Reveal Specific Gene Family Losses and Gains during Adaptation to Specific Infection Lifestyles. Genome Biol Evol 2016; 8:1467-81. [PMID: 27189990 PMCID: PMC4898803 DOI: 10.1093/gbe/evw089] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
Members from Colletotrichum genus adopt a diverse range of lifestyles during infection of plants and represent a group of agriculturally devastating pathogens. In this study, we present the draft genome of Colletotrichum incanum from the spaethianum clade of Colletotrichum and the comparative analyses with five other Colletotrichum species from distinct lineages. We show that the C. incanum strain, originally isolated from Japanese daikon radish, is able to infect both eudicot plants, such as certain ecotypes of the eudicot Arabidopsis, and monocot plants, such as lily. Being closely related to Colletotrichum species both in the graminicola clade, whose members are restricted strictly to monocot hosts, and to the destructivum clade, whose members are mostly associated with dicot infections, C. incanum provides an interesting model system for comparative genomics to study how fungal pathogens adapt to monocot and dicot hosts. Genus-wide comparative genome analyses reveal that Colletotrichum species have tailored profiles of their carbohydrate-degrading enzymes according to their infection lifestyles. In addition, we show evidence that positive selection acting on secreted and nuclear localized proteins that are highly conserved may be important in adaptation to specific hosts or ecological niches.
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Affiliation(s)
- Pamela Gan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Mari Narusaka
- Research Institute for Biological Sciences Okayama, Okayama, Japan
| | | | - Ayako Tsushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113–0033, Japan
| | | | | | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113–0033, Japan
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23
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Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:776. [PMID: 26442085 DOI: 10.3389/fpls.2015.00776issn=1664-462x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 05/25/2023]
Abstract
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.
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Affiliation(s)
- Thomas Badet
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441 Castanet-Tolosan, France ; Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594 Castanet-Tolosan, France
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24
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Árnason E, Halldórsdóttir K. Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models. PeerJ 2015; 3:e786. [PMID: 25755922 PMCID: PMC4349156 DOI: 10.7717/peerj.786] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 01/11/2023] Open
Abstract
High-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and the entailing genetic load of replacing alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with FST > 0.8 between regions whereas neutral loci show no differentiation. This is evidence of natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. The unfolded site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales vary with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show that times scales are faster than under the Kingman coalescent.
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Affiliation(s)
- Einar Árnason
- Institute of Life and Environmental Sciences, University of Iceland , Reykjavík , Iceland
| | - Katrín Halldórsdóttir
- Institute of Life and Environmental Sciences, University of Iceland , Reykjavík , Iceland
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25
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Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:776. [PMID: 26442085 PMCID: PMC4585107 DOI: 10.3389/fpls.2015.00776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/10/2015] [Indexed: 05/04/2023]
Abstract
Fungal plant pathogens produce secreted proteins adapted to function outside fungal cells to facilitate colonization of their hosts. In many cases such as for fungi from the Sclerotiniaceae family the repertoire and function of secreted proteins remains elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic lifestyle with a low optimal growth temperature, a narrow host range and geographic distribution. To spread successfully, S. borealis must synthesize proteins adapted to function in its specific environment. The search for signatures of adaptation to S. borealis lifestyle may therefore help revealing proteins critical for colonization of the environment by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae species. We found that enrichment in Thr, depletion in Glu and Lys, and low disorder frequency in hot loops are significantly associated with S. borealis proteins. We designed an index to report bias in these properties and found that high index proteins were enriched among secreted proteins in the three Sclerotiniaceae fungi. High index proteins were also enriched in function associated with plant colonization in S. borealis, and in in planta-induced genes in S. sclerotiorum. We highlight a novel putative antifreeze protein and a novel putative lytic polysaccharide monooxygenase identified through our pipeline as candidate proteins involved in colonization of the environment. Our findings suggest that similar protein signatures associate with S. borealis lifestyle and with secretion in the Sclerotiniaceae. These signatures may be useful for identifying proteins of interest as targets for the management of plant diseases.
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Affiliation(s)
- Thomas Badet
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, UMR2594Castanet-Tolosan, France
- *Correspondence: Sylvain Raffaele, Laboratoire des Interactions Plante Micro-organismes, 24 Chemin de Borde Rouge – Auzeville, 31326 Castanet Tolosan, France
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