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Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
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Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
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2
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Zhan XY, Zha GF, He Y. Evolutionary dissection of monkeypox virus: Positive Darwinian selection drives the adaptation of virus-host interaction proteins. Front Cell Infect Microbiol 2023; 12:1083234. [PMID: 36710983 PMCID: PMC9880225 DOI: 10.3389/fcimb.2022.1083234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023] Open
Abstract
The emerging and ongoing outbreak of human monkeypox (hMPX) in 2022 is a serious global threat. An understanding of the evolution of the monkeypox virus (MPXV) at the single-gene level may provide clues for exploring the unique aspects of the current outbreak: rapidly expanding and sustained human-to-human transmission. For the current investigation, alleles of 156 MPXV coding genes (which account for >95% of the genomic sequence) have been gathered from roughly 1,500 isolates, including those responsible for the previous outbreaks. Using a range of molecular evolution approaches, we demonstrated that intra-species homologous recombination has a negligible effect on MPXV evolution. Despite the fact that the majority of the MPXV genes (64.10%) were subjected to negative selection at the whole gene level, 10 MPXV coding genes (MPXVgp004, 010, 012, 014, 044, 098, 138, 178, 188, and 191) were found to have a total of 15 codons or amino acid sites that are known to evolve under positive Darwinian selection. Except for MPXVgp138, almost all of these genes encode proteins that interact with the host. Of these, five ankyrin proteins (MPXVgp004, 010, 012, 178, and 188) and one Bcl-2-like protein (MPXVgp014) are involved in poxviruses' host range determination. We discovered that the majority (80%) of positive amino acid substitutions emerged several decades ago, indicating that these sites have been under constant selection pressure and that more adaptable alleles have been circulating in the natural reservoir. This finding was also supported by the minimum spanning networks of the gene alleles. The three positive amino acid substitutions (T/A426V in MPXVgp010, A423D in MPXVgp012, and S105L in MPXVgp191) appeared in 2019 or 2022, indicating that they would be crucial for the virus' eventual adaptation to humans. Protein modeling suggests that positive amino acid substitutions may affect protein functions in a variety of ways. Further study should focus on revealing the biological effects of positive amino acid substitutions in the genes for viral adaptation to humans, virulence, transmission, and so on. Our study advances knowledge of MPXV's adaptive mechanism and provides insights for exploring factors that are responsible for the unique aspects of the current outbreak.
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Affiliation(s)
- Xiao-Yong Zhan
- *Correspondence: Xiao-Yong Zhan, ; Gao-Feng Zha, ; Yulong He,
| | - Gao-Feng Zha
- *Correspondence: Xiao-Yong Zhan, ; Gao-Feng Zha, ; Yulong He,
| | - Yulong He
- *Correspondence: Xiao-Yong Zhan, ; Gao-Feng Zha, ; Yulong He,
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3
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Zhan XY, Yang JL, Zhou X, Qian YC, Huang K, Sun H, Wang H, Leng Y, Huang B, He Y. Virulence effector SidJ evolution in Legionella pneumophila is driven by positive selection and intragenic recombination. PeerJ 2021; 9:e12000. [PMID: 34458026 PMCID: PMC8378335 DOI: 10.7717/peerj.12000] [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: 06/02/2021] [Accepted: 07/27/2021] [Indexed: 11/20/2022] Open
Abstract
Effector proteins translocated by the Dot/Icm type IV secretion system determine the virulence of Legionella pneumophila (L. pneumophila). Among these effectors, members of the SidE family (SidEs) regulate several cellular processes through a unique phosphoribosyl ubiquitination mechanism mediated by another effector, SidJ. Host-cell calmodulin (CaM) activates SidJ to glutamylate the SidEs of ubiquitin (Ub) ligases and to make a balanced Ub ligase activity. Given the central role of SidJ in this regulatory process, studying the nature of evolution of sidJ is important to understand the virulence of L. pneumophila and the interaction between the bacteria and its hosts. By studying sidJ from a large number of L. pneumophila strains and using various molecular evolution algorithms, we demonstrated that intragenic recombination drove the evolution of sidJ and contributed to sidJ diversification. Additionally, we showed that four codons of sidJ which are located in the N-terminal (NTD) (codons 58 and 200) and C-terminal (CTD) (codons 868 and 869) domains, but not in the kinase domain (KD) had been subjected to strong positive selection pressure, and variable mutation profiles of these codons were identified. Protein structural modeling of SidJ provided possible explanations for these mutations. Codons 868 and 869 mutations might engage in regulating the interactions of SidJ with CaM through hydrogen bonds and affect the CaM docking to SidJ. Mutation in codon 58 of SidJ might affect the distribution of main-chain atoms that are associated with the interaction with CaM. In contrast, mutations in codon 200 might influence the α-helix stability in the NTD. These mutations might be important to balance Ub ligase activity for different L. pneumophila hosts. This study first reported that intragenic recombination and positive Darwinian selection both shaped the genetic plasticity of sidJ, contributing to a deeper understanding of the adaptive mechanisms of this intracellular bacterium to different hosts.
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Affiliation(s)
- Xiao-Yong Zhan
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jin-Lei Yang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xuefu Zhou
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yi-Chao Qian
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ke Huang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Honghua Sun
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Huacheng Wang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yang Leng
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Bihui Huang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yulong He
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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4
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Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102011. [PMID: 33677388 DOI: 10.1016/j.pbi.2021.102011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 05/13/2023]
Abstract
The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effector activity to trigger immunity (effector-triggered immunity; ETI). Here we discuss how this ongoing ETS-ETI cycle has shaped the natural diversity of both plant resistance proteins and pathogen effectors. We focus on the evolutionary forces that drive the diversification of the molecules that determine the outcome of plant-pathogen interactions and introduce the concept of metapopulation dynamics (i.e., the introduction of genetic variation from conspecific organisms in different populations) as an alternative mechanism that can introduce and maintain diversity in both host and pathogen populations.
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Affiliation(s)
- Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Clare Breit-McNally
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
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5
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Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, Stam R, van Oosterhout C, Fairhead S, Heal R, Cocker JM, Bhanvadia S, Barrett W, Wu CH, Adachi H, Song T, Kamoun S, Vleeshouwers VGAA, Tomlinson L, Wulff BBH, Jones JDG. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. NATURE PLANTS 2021; 7:198-208. [PMID: 33574576 PMCID: PMC7116783 DOI: 10.1038/s41477-021-00854-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologues and paralogues. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogues and alleles of the recognized effector, facilitating durable resistance against P. infestans.
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Affiliation(s)
- Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- US Department of Agriculture-Agricultural Research Service, Madison, WI, USA
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Bayer Crop Science, Chesterfield, MO, USA
| | - Agnieszka I Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Remco Stam
- Phytopathology, Technical University Munich, Freising, Germany
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan M Cocker
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- University of Hull, Hull, UK
| | - Shivani Bhanvadia
- Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
| | - William Barrett
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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6
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Tichkule S, Jex AR, van Oosterhout C, Sannella AR, Krumkamp R, Aldrich C, Maiga-Ascofare O, Dekker D, Lamshöft M, Mbwana J, Rakotozandrindrainy N, Borrmann S, Thye T, Schuldt K, Winter D, Kremsner PG, Oppong K, Manouana P, Mbong M, Gesase S, Minja DTR, Mueller I, Bahlo M, Nader J, May J, Rakotozandrindrain R, Adegnika AA, Lusingu JPA, Amuasi J, Eibach D, Caccio SM. Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa. Microb Genom 2021; 7:mgen000493. [PMID: 33355530 PMCID: PMC8115899 DOI: 10.1099/mgen.0.000493] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/26/2020] [Indexed: 12/02/2022] Open
Abstract
Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 (gp60) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive exploration of the metapopulation structure and evolution based on whole-genome data has yet to be performed. Here, we sequenced and analysed the genomes of 26 C. hominis isolates, representing different gp60 subtypes, collected at rural sites in Gabon, Ghana, Madagascar and Tanzania. Phylogenetic and cluster analyses based on single-nucleotide polymorphisms showed that isolates predominantly clustered by their country of origin, irrespective of their gp60 subtype. We found a significant isolation-by-distance signature that shows the importance of local transmission, but we also detected evidence of hybridization between isolates of different geographical regions. We identified 37 outlier genes with exceptionally high nucleotide diversity, and this group is significantly enriched for genes encoding extracellular proteins and signal peptides. Furthermore, these genes are found more often than expected in recombinant regions, and they show a distinct signature of positive or balancing selection. We conclude that: (1) the metapopulation structure of C. hominis can only be accurately captured by whole-genome analyses; (2) local anthroponotic transmission underpins the spread of this pathogen in Africa; (3) hybridization occurs between distinct geographical lineages; and (4) genetic introgression provides novel substrate for positive or balancing selection in genes involved in host-parasite coevolution.
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Affiliation(s)
- Swapnil Tichkule
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Aaron R. Jex
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Anna Rosa Sannella
- Department of Infectious Disease, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Cassandra Aldrich
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich 80802, Germany
| | - Oumou Maiga-Ascofare
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, KNUST, Kumasi, Ghana
| | - Denise Dekker
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Maike Lamshöft
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Joyce Mbwana
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | | | - Steffen Borrmann
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
- Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
| | - Thorsten Thye
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Kathrin Schuldt
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Doris Winter
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Peter G. Kremsner
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
- Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
| | - Kwabena Oppong
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, KNUST, Kumasi, Ghana
| | - Prince Manouana
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
| | - Mirabeau Mbong
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
| | - Samwel Gesase
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Daniel T. R. Minja
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - Ivo Mueller
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Melanie Bahlo
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Johanna Nader
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | | | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
- Institut für Tropenmedizin and German Center for Infection Research, partner site Tübingen, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
| | - John P. A. Lusingu
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, College of Health Sciences, KNUST, Kumasi, Ghana
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine Hamburg, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Germany
| | - Simone Mario Caccio
- Department of Infectious Disease, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
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7
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Riaz S, Menéndez CM, Tenscher A, Pap D, Walker MA. Genetic mapping and survey of powdery mildew resistance in the wild Central Asian ancestor of cultivated grapevines in Central Asia. HORTICULTURE RESEARCH 2020; 7:104. [PMID: 32637132 PMCID: PMC7326912 DOI: 10.1038/s41438-020-0335-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 04/01/2020] [Accepted: 05/01/2020] [Indexed: 05/21/2023]
Abstract
Cultivated grapevines (Vitis vinifera) lack resistance to powdery mildew (PM) with few exceptions. Resistance to this pathogen within V. vinifera has been reported in earlier studies and identified as the Ren1 locus in two Central Asian table grape accessions. Other PM-resistant cultivated varieties and accessions of the wild ancestor V. vinifera subsp. sylvestris were soon identified raising questions regarding the origin of the resistance. In this study, F1 breeding populations were developed with a PM susceptible V. vinifera subsp. vinifera breeding line and a PM-resistant subsp. sylvestris accession. Genotyping was carried out with five Ren1 locus linked SSR markers. A PM resistance locus explaining up to 96% of the phenotypic variation was identified in the same genomic position, where the Ren1 locus was previously reported. New SSR marker alleles linked with the resistance locus were identified. We report results of PM resistance in multiple accessions of subsp. sylvestris collected as seed lots or cuttings from five countries in the Caucasus and Central Asia. A total of 20 females from 11 seed lots and 19 males from nine seed lots collected from Georgia, Armenia, and Azerbaijan were resistant to PM. Three male and one female plant collected as cuttings from Afghanistan and Iran were also resistant to PM. Allelic analysis of markers linked with the Ren1 locus in conjunction with disease evaluation data found a high diversity of allelic haplotypes, which are only possible via recombination events occurring over a long time period. Sequence analysis of two alleles of the SSR marker that cosegregates with the resistance found SNPs that were present in the wild progenitor and in cultivated forms. Variable levels of PM resistance among the tested accessions were also observed. These lines of evidence suggest that the powdery mildew fungus may have been present in Asia for a longer time than currently thought, giving the wild progenitor V. vinifera subsp. sylvestris time to coevolve with and develop resistance to this pathogen.
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Affiliation(s)
- Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Cristina M. Menéndez
- Instituto de Ciencias de la Vid y del Vino (ICVV), Universidad de La Rioja-CSIC-Gobierno de La Rioja, Carretera de Burgos Km, 6, Finca La Grajera, Logroño, La Rioja 26007 Spain
| | - Alan Tenscher
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - Daniel Pap
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
| | - M. Andrew Walker
- Department of Viticulture and Enology, University of California, Davis, CA 95616 USA
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8
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Evidence for Adaptive Introgression of Disease Resistance Genes Among Closely Related Arabidopsis Species. G3-GENES GENOMES GENETICS 2017. [PMID: 28630104 PMCID: PMC5555472 DOI: 10.1534/g3.117.043984] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The generation and maintenance of functional variation in the pathogen defense system of plants is central to the constant evolutionary battle between hosts and parasites. If a species is susceptible to a given pathogen, hybridization and subsequent introgression of a resistance allele from a related species can potentially be an important source of new immunity and is therefore expected to be selected for in a process referred to as adaptive introgression. Here, we survey sequence variation in 10 resistance (R-) genes and compare them with 37 reference genes in natural populations of the two closely related and interfertile species: Arabidopsis lyrata and A. halleri. The R-genes are highly polymorphic in both species and show clear signs of trans-species polymorphisms. We show that A. lyrata and A. halleri have had a history of limited introgression for the reference genes. For the R-genes, the introgression rate has been significantly higher than for the reference genes, resulting in fewer fixed differences between species and a higher sharing of identical haplotypes. We conclude that R-genes likely cross the species boundaries at a higher rate than reference genes and therefore also that some of the increased diversity and trans-specific polymorphisms in R-genes is due to adaptive introgression.
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9
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Eimes JA, Lee SI, Townsend AK, Jablonski P, Nishiumi I, Satta Y. Early Duplication of a Single MHC IIB Locus Prior to the Passerine Radiations. PLoS One 2016; 11:e0163456. [PMID: 27658204 PMCID: PMC5033386 DOI: 10.1371/journal.pone.0163456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/08/2016] [Indexed: 01/01/2023] Open
Abstract
A key characteristic of MHC genes is the persistence of allelic lineages over macroevolutionary periods, often through multiple speciation events. This phenomenon, known as trans-species polymorphism (TSP), is well documented in several major taxonomic groups, but has less frequently been observed in birds. The order Passeriformes is arguably the most successful terrestrial vertebrate order in terms of diversity of species and ecological range, but the reasons for this success remain unclear. Passerines exhibit the most highly duplicated MHC genes of any major vertebrate taxonomic group, which may generate increased immune response relative to other avian orders with fewer MHC loci. Here, we describe phylogenetic patterns of the MHC IIB in the passerine family Corvidae. Our results indicate wide-spread TSP within this family, with at least four supported MHC IIB allelic lineages that predate speciation by many millions of years. Markov chain Monte Carlo simulations indicate that divergence of these lineages occurred near the time of the divergence of the Passeriformes and other avian orders. We suggest that the current MHC diversity observed in passerines is due in part to the multiple duplication of a single MHC locus, DAB1, early in passerine evolution and that subsequent duplications of these paralogues have contributed to the enormous success of this order by increasing their ability to recognize and mount immune responses to novel pathogens.
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Affiliation(s)
- John A. Eimes
- Seoul National University, Department of Biological Sciences, Seoul, Korea
| | - Sang-im Lee
- Seoul National University, Institute of Advanced Machines and Design, Seoul, Korea
- * E-mail:
| | - Andrea K. Townsend
- Hamilton College, Department of Biology, Clinton, NY, United States of America
| | - Piotr Jablonski
- Seoul National University, Department of Biological Sciences, Seoul, Korea
| | - Isao Nishiumi
- National Museum of Nature and Science, Department of Zoology, Tsukuba, Japan
| | - Yoko Satta
- The Graduate University for Advanced Studies, Department of Evolutionary Studies of Biosystems, Hayama, Japan
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10
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Wang D, Wang X, Mei Y, Dong H. The wheat homolog of putative nucleotide-binding site-leucine-rich repeat resistance gene TaRGA contributes to resistance against powdery mildew. Funct Integr Genomics 2016; 16:115-26. [PMID: 26815536 DOI: 10.1007/s10142-015-0471-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 11/20/2015] [Accepted: 12/21/2015] [Indexed: 01/20/2023]
Abstract
Powdery mildew, one of the most destructive wheat diseases worldwide, is caused by Blumeria graminis f. sp. tritici (Bgt), a fungal species with a consistently high mutation rate that makes individual resistance (R) genes ineffective. Therefore, effective resistance-related gene cloning is vital for breeding and studying the resistance mechanisms of the disease. In this study, a putative nucleotide-binding site-leucine-rich repeat (NBS-LRR) R gene (TaRGA) was cloned using a homology-based cloning strategy and analyzed for its effect on powdery mildew disease and wheat defense responses. Real-time reverse transcription-PCR (RT-PCR) analyses revealed that a Bgt isolate 15 and salicylic acid stimulation significantly induced TaRGA in the resistant variety. Furthermore, the silencing of TaRGA in powdery mildew-resistant plants increased susceptibility to Bgt15 and prompted conidia propagation at the infection site. However, the expression of TaRGA in leaf segments after single-cell transient expression assay highly increased the defense responses to Bgt15 by enhancing callose deposition and phenolic autofluorogen accumulation at the pathogen invading sites. Meanwhile, the expression of pathogenesis-related genes decreased in the TaRGA-silenced plants and increased in the TaRGA-transient-overexpressing leaf segments. These results implied that the TaRGA gene positively regulates the defense response to powdery mildew disease in wheat.
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Affiliation(s)
- Defu Wang
- College of Life Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.,National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaobing Wang
- National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Mei
- National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hansong Dong
- National Ministry of Education Key Laboratory of Integrated Management of Crop Diseases and Insect Pests, Nanjing Agricultural University, Nanjing, 210095, China.
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11
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Ward BJ, van Oosterhout C. HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Mol Ecol Resour 2015; 16:534-9. [PMID: 26394708 DOI: 10.1111/1755-0998.12469] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 11/29/2022]
Abstract
HYBRIDCHECK is a software package to visualize the recombination signal in large DNA sequence data set, and it can be used to analyse recombination, genetic introgression, hybridization and horizontal gene transfer. It can scan large (multiple kb) contigs and whole-genome sequences of three or more individuals. HYBRIDCHECK is written in the r software for OS X, Linux and Windows operating systems, and it has a simple graphical user interface. In addition, the r code can be readily incorporated in scripts and analysis pipelines. HYBRIDCHECK implements several ABBA-BABA tests and visualizes the effects of hybridization and the resulting mosaic-like genome structure in high-density graphics. The package also reports the following: (i) the breakpoint positions, (ii) the number of mutations in each introgressed block, (iii) the probability that the identified region is not caused by recombination and (iv) the estimated age of each recombination event. The divergence times between the donor and recombinant sequence are calculated using a JC, K80, F81, HKY or GTR correction, and the dating algorithm is exceedingly fast. By estimating the coalescence time of introgressed blocks, it is possible to distinguish between hybridization and incomplete lineage sorting. HYBRIDCHECK is libré software and it and its manual are free to download from http://ward9250.github.io/HybridCheck/.
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Affiliation(s)
- Ben J Ward
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich, NR4 7TJ, UK
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