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Mullett MS, Harris AR, Scanu B, Van Poucke K, LeBoldus J, Stamm E, Bourret TB, Christova PK, Oliva J, Redondo MA, Talgø V, Corcobado T, Milenković I, Jung MH, Webber J, Heungens K, Jung T. Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae. MOLECULAR PLANT PATHOLOGY 2024; 25:e13450. [PMID: 38590129 PMCID: PMC11002350 DOI: 10.1111/mpp.13450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping-by-sequencing. Coalescent-based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide.
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Affiliation(s)
- Martin S. Mullett
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | | | - Bruno Scanu
- Department of Agricultural SciencesUniversity of SassariSassariItaly
| | - Kris Van Poucke
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitMerelbekeBelgium
| | - Jared LeBoldus
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
- Department of Forest Engineering, Resources, and ManagementOregon State UniversityCorvallisOregonUSA
| | - Elizabeth Stamm
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Tyler B. Bourret
- USDA‐ARS Mycology and Nematology Genetic Diversity and Biology LaboratoryBeltsvilleMarylandUSA
- Department of Plant PathologyUC DavisDavisCaliforniaUSA
| | | | - Jonás Oliva
- Department of Agricultural and Forest Sciences and EngineeringUniversity of LleidaLleidaSpain
- Joint Research Unit CTFC–AGROTECNIO–CERCALleidaSpain
| | - Miguel A. Redondo
- National Bioinformatics Infrastructure Sweden, Science for Life LaboratorySweden
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Venche Talgø
- Division of Biotechnology and Plant HealthNorwegian Institute of Bioeconomy Research (NIBIO)ÅsNorway
| | - Tamara Corcobado
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | - Ivan Milenković
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | - Marília Horta Jung
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | | | - Kurt Heungens
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitMerelbekeBelgium
| | - Thomas Jung
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
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Möller H, Coetzee B, van Niekerk J, Rose LJ. Reference Genome Resource for the Citrus Pathogen Phytophthora citrophthora. J Genomics 2024; 12:14-18. [PMID: 38164508 PMCID: PMC10751748 DOI: 10.7150/jgen.89324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/12/2023] [Indexed: 01/03/2024] Open
Abstract
Phytophthora citrophthora is an oomycete pathogen that infects citrus. Its occurrence in citrus-growing regions worldwide is considered a major contributor to crop losses. This study presents a high-quality genome resource for P. citrophthora, which was generated using PacBio HiFi long-read high-throughput sequencing technology. We successfully assembled a 48.5 Mb genome containing 16,409 protein-coding genes from high-quality reads. This marks the first complete genome assembly of P. citrophthora, providing a valuable resource to enhance the understanding of pathogenic behaviour and fungicide sensitivity of this destructive citrus pathogen.
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Affiliation(s)
- Heike Möller
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Beatrix Coetzee
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Jan van Niekerk
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa
| | - Lindy Joy Rose
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Cox MP, Guo Y, Winter DJ, Sen D, Cauldron NC, Shiller J, Bradley EL, Ganley AR, Gerth ML, Lacey RF, McDougal RL, Panda P, Williams NM, Grunwald NJ, Mesarich CH, Bradshaw RE. Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families. Front Microbiol 2022; 13:1038444. [PMID: 36406440 PMCID: PMC9667082 DOI: 10.3389/fmicb.2022.1038444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/11/2022] [Indexed: 01/25/2023] Open
Abstract
Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
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Affiliation(s)
- Murray P. Cox
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yanan Guo
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J. Winter
- Institute of Environmental Science and Research (ESR), Porirua, New Zealand
| | | | - Nicholas C. Cauldron
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | | | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Austen R. Ganley
- School of Biological Sciences and Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Monica L. Gerth
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Randy F. Lacey
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | | | | | - Niklaus J. Grunwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, OR, United States
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
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Oresegun DR, Thorpe P, Benavente ED, Campino S, Muh F, Moon RW, Clark TG, Cox-Singh J. De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. Front Genet 2022; 13:855052. [PMID: 35677565 PMCID: PMC9169567 DOI: 10.3389/fgene.2022.855052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/15/2022] [Indexed: 12/31/2022] Open
Abstract
Plasmodium knowlesi, a malaria parasite of Old World macaque monkeys, is used extensively to model Plasmodium biology. Recently, P. knowlesi was found in the human population of Southeast Asia, particularly Malaysia. P. knowlesi causes uncomplicated to severe and fatal malaria in the human host with features in common with the more prevalent and virulent malaria caused by Plasmodium falciparum. As such, P. knowlesi presents a unique opportunity to develop experimental translational model systems for malaria pathophysiology informed by clinical data from same-species human infections. Experimental lines of P. knowlesi represent well-characterized genetically stable parasites, and to maximize their utility as a backdrop for understanding malaria pathophysiology, genetically diverse contemporary clinical isolates, essentially wild-type, require comparable characterization. The Oxford Nanopore PCR-free long-read sequencing platform was used to sequence and de novo assemble P. knowlesi genomes from frozen clinical samples. The sequencing platform and assembly pipelines were designed to facilitate capturing data and describing, for the first time, P. knowlesi schizont-infected cell agglutination (SICA) var and Knowlesi-Interspersed Repeats (kir) multiple gene families in parasites acquired from nature. The SICAvar gene family members code for antigenically variant proteins analogous to the virulence-associated P. falciparum erythrocyte membrane protein (PfEMP1) multiple var gene family. Evidence presented here suggests that the SICAvar family members have arisen through a process of gene duplication, selection pressure, and variation. Highly evolving genes including PfEMP1family members tend to be restricted to relatively unstable sub-telomeric regions that drive change with core genes protected in genetically stable intrachromosomal locations. The comparable SICAvar and kir gene family members are counter-intuitively located across chromosomes. Here, we demonstrate that, in contrast to conserved core genes, SICAvar and kir genes occupy otherwise gene-sparse chromosomal locations that accommodate rapid evolution and change. The novel methods presented here offer the malaria research community not only new tools to generate comprehensive genome sequence data from small clinical samples but also new insight into the complexity of clinically important real-world parasites.
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Affiliation(s)
- Damilola R. Oresegun
- Division of Infection and Global Health, School of Medicine, University of St Andrews, Scotland, United Kingdom
| | - Peter Thorpe
- Division of Infection and Global Health, School of Medicine, University of St Andrews, Scotland, United Kingdom
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Fauzi Muh
- Division of Infection and Global Health, School of Medicine, University of St Andrews, Scotland, United Kingdom
| | - Robert William Moon
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Taane Gregory Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Janet Cox-Singh
- Division of Infection and Global Health, School of Medicine, University of St Andrews, Scotland, United Kingdom
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