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Foster ZSL, Tupper AS, Press CM, Grünwald NJ. Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data. PLoS Comput Biol 2024; 20:e1012139. [PMID: 38768250 PMCID: PMC11142669 DOI: 10.1371/journal.pcbi.1012139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/31/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Recent pandemics like COVID-19 highlighted the importance of rapidly developing diagnostics to detect evolving pathogens. CRISPR-Cas technology has recently been used to develop diagnostic assays for sequence-specific recognition of DNA or RNA. These assays have similar sensitivity to the gold standard qPCR but can be deployed as easy to use and inexpensive test strips. However, the discovery of diagnostic regions of a genome flanked by conserved regions where primers can be designed requires extensive bioinformatic analyses of genome sequences. We developed the Python package krisp to aid in the discovery of primers and diagnostic sequences that differentiate groups of samples from each other, using either unaligned genome sequences or a variant call format (VCF) file as input. Krisp has been optimized to handle large datasets by using efficient algorithms that run in near linear time, use minimal RAM, and leverage parallel processing when available. The validity of krisp results has been demonstrated in the laboratory with the successful design of a CRISPR diagnostic assay to distinguish the sudden oak death pathogen Phytophthora ramorum from closely related Phytophthora species. Krisp is released open source under a permissive license with all the documentation needed to quickly design CRISPR-Cas diagnostic assays.
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Affiliation(s)
- Zachary S. L. Foster
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Andrew S. Tupper
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Caroline M. Press
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
| | - Niklaus J. Grünwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, Oregon, United States of America
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2
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Zhou Z, Yang X, Wu C, Chen Z, Dai T. Whole-Genome Sequence Resource of Phytophthora pini, the Causal Pathogen of Foliage Blight and Shoot Dieback of Rhododendron pulchrum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:944-948. [PMID: 36074693 DOI: 10.1094/mpmi-05-22-0106-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Ziwei Zhou
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiao Yang
- Plant and Pest Diagnostic Clinic, Department of Plant Industry, Clemson University, Pendleton, SC, U.S.A
| | - Cuiping Wu
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, Jiangsu, China
| | - Zhenpeng Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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3
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Thorpe P, Vetukuri RR, Hedley PE, Morris J, Whisson MA, Welsh LRJ, Whisson SC. Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae. G3 (BETHESDA, MD.) 2021; 11:jkab282. [PMID: 34849788 PMCID: PMC8527500 DOI: 10.1093/g3journal/jkab282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/22/2021] [Indexed: 11/14/2022]
Abstract
Species of Phytophthora, plant pathogenic eukaryotic microbes, can cause disease on many tree species. Genome sequencing of species from this genus has helped to determine components of their pathogenicity arsenal. Here, we sequenced genomes for two widely distributed species, Phytophthora pseudosyringae and Phytophthora boehmeriae, yielding genome assemblies of 49 and 40 Mb, respectively. We identified more than 270 candidate disease promoting RXLR effector coding genes for each species, and hundreds of genes encoding candidate plant cell wall degrading carbohydrate active enzymes (CAZymes). These data boost genome sequence representation across the Phytophthora genus, and form resources for further study of Phytophthora pathogenesis.
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Affiliation(s)
- Peter Thorpe
- School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, SE-234 22, Sweden
| | - Pete E Hedley
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jenny Morris
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | | | - Lydia R J Welsh
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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4
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Wang S, Vetukuri RR, Kushwaha SK, Hedley PE, Morris J, Studholme DJ, Welsh LRJ, Boevink PC, Birch PRJ, Whisson SC. Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae. MOLECULAR PLANT PATHOLOGY 2021; 22:954-968. [PMID: 34018655 PMCID: PMC8295517 DOI: 10.1111/mpp.13072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 05/29/2023]
Abstract
Phytophthora species cause some of the most serious diseases of trees and threaten forests in many parts of the world. Despite the generation of genome sequence assemblies for over 10 tree-pathogenic Phytophthora species and improved detection methods, there are many gaps in our knowledge of how these pathogens interact with their hosts. To facilitate cell biology studies of the infection cycle we examined whether the tree pathogen Phytophthora kernoviae could infect the model plant Nicotiana benthamiana. We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells. Haustoria were also formed in infected cells of natural hosts, Rhododendron ponticum and European beech (Fagus sylvatica). We analysed the transcriptome of P. kernoviae in cultured mycelia, spores, and during infection of N. benthamiana, and detected 12,559 transcripts. Of these, 1,052 were predicted to encode secreted proteins, some of which may function as effectors to facilitate disease development. From these, we identified 87 expressed candidate RXLR (Arg-any amino acid-Leu-Arg) effectors. We transiently expressed 12 of these as GFP fusions in N. benthamiana leaves and demonstrated that nine significantly enhanced P. kernoviae disease progression and diversely localized to the cytoplasm, nucleus, nucleolus, and plasma membrane. Our results show that N. benthamiana can be used as a model host plant for studying this tree pathogen, and that the interaction likely involves suppression of host immune responses by RXLR effectors. These results establish a platform to expand the understanding of Phytophthora tree diseases.
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Affiliation(s)
- Shumei Wang
- Division of Plant SciencesUniversity of DundeeJames Hutton InstituteInvergowrie, DundeeUK
| | - Ramesh R. Vetukuri
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
| | - Sandeep K. Kushwaha
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
- National Institute of Animal BiotechnologyHyderabadIndia
| | - Pete E. Hedley
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Jenny Morris
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
| | - Lydia R. J. Welsh
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Paul R. J. Birch
- Division of Plant SciencesUniversity of DundeeJames Hutton InstituteInvergowrie, DundeeUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
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5
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de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol Ecol 2021; 96:5904760. [PMID: 32918444 PMCID: PMC7585586 DOI: 10.1093/femsec/fiaa184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany.,Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany.,Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.,Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
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6
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de Vries S, de Vries J. A Global Survey of Carbohydrate Esterase Families 1 and 10 in Oomycetes. Front Genet 2020; 11:756. [PMID: 32849784 PMCID: PMC7427535 DOI: 10.3389/fgene.2020.00756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022] Open
Abstract
Carbohydrate-active enzymes (CAZymes) are a cornerstone in the phytopathogenicity of filamentous microbes. CAZymes are required for every step of a successful infection cycle-from penetration, to nutrient acquisition (during colonization), to exit and dispersal. Yet, CAZymes are not a unique feature of filamentous pathogens. They are found across eukaryotic genomes and including, for example, saprotrophic relatives of major pathogens. Comparative genomics and functional analyses revealed that CAZyme content is shaped by a multitude of factors, including utilized substrate, lifestyle, and host preference. Yet, family size alone says little about usage. Indeed, in a previous study, we found that genes putatively coding for the CAZyme families of carbohydrate esterase (CE)1 and CE10, while not specifically enriched in number, were suggested to have lifestyle-specific gene expression patterns. Here, we used comparative genomics and a clustering approach to understand how the repertoire of the CE1- and CE10-encoding gene families is shaped across oomycete evolution. These data are combined with comparative transcriptomic analyses across homologous clusters within the gene families. We find that CE1 and CE10 have been reduced in number in biotrophic oomycetes independent of the phylogenetic relationship of the biotrophs to each other. The reduction in CE1 is different from that observed for CE10: While in CE10 specific clusters of homologous sequences show convergent reduction, CE1 reduction is caused by species-specific losses. Comparative transcriptomics revealed that some clusters of CE1 or CE10 sequences have a higher expression than others, independent of the species composition within them. Further, we find that CE1- and CE10-encoding genes are mainly induced in plant pathogens and that some homologous genes show lifestyle-specific gene expression levels during infection, with hemibiotrophs showing the highest expression levels.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göettingen, Göettingen, Germany
- Göettingen Center for Molecular Biosciences (GZMB), University of Göettingen, Göettingen, Germany
- Campus Institute Data Science, University of Göettingen, Göettingen, Germany
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7
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Grünwald NJ, LeBoldus JM, Hamelin RC. Ecology and Evolution of the Sudden Oak Death Pathogen Phytophthora ramorum. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:301-321. [PMID: 31226018 DOI: 10.1146/annurev-phyto-082718-100117] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sudden oak and sudden larch death pathogen Phytophthora ramorum emerged simultaneously in the United States on oak and in Europe on Rhododendron in the 1990s. This pathogen has had a devastating impact on larch plantations in the United Kingdom as well as mixed conifer and oak forests in the Western United States. Since the discovery of this pathogen, a large body of research has provided novel insights into the emergence, epidemiology, and genetics of this pandemic. Genetic and genomic resources developed for P. ramorum have been instrumental in improving our understanding of the epidemiology, evolution, and ecology of this disease. The recent reemergence of EU1 in the United States and EU2 in Europe and the discovery of P. ramorum in Asia provide renewed impetus for research on the sudden oak death pathogen.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA;
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR 97331-5704, USA
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Faculté de Foresterie et de Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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8
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Studholme DJ, Panda P, Sanfuentes Von Stowasser E, González M, Hill R, Sambles C, Grant M, Williams NM, McDougal RL. Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome. MOLECULAR PLANT PATHOLOGY 2019; 20:423-431. [PMID: 30390404 PMCID: PMC6637878 DOI: 10.1111/mpp.12765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Genome sequences were generated for six oomycete isolates collected from forests in Valdivia, Chile. Three of the isolates were identified morphologically as Phytophthora kernoviae, whereas two were similar to other clade 10 Phytophthora species. One isolate was tentatively identified as Nothophytophthora valdiviana based on nucleotide sequence similarity in the cytochrome oxidase 1 gene. This is the first genome sequence for this recently described genus. The genome assembly was more fragmented and contained many duplicated genes when compared with the other Phytophthora sequences. Comparative analyses were performed with genomic sequences of the P. kernoviae isolates from the UK and New Zealand. Although the potential New Zealand origin of P. kernoviae has been suggested, new isolations from Chile had cast doubt on this hypothesis. We present evidence supporting P. kernoviae as having originated in New Zealand. However, investigation of the diversity of oomycete species in Chile has been limited and warrants further exploration. We demonstrate the expediency of genomic analyses in determining phylogenetic relationships between isolates within new and often scantly represented taxonomic groups, such as Phytophthora clade 10 and Nothophytophthora. Data are available on GenBank via BioProject accession number PRJNA352331.
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Affiliation(s)
| | - Preeti Panda
- Scion (New Zealand Forest Research Institute, Ltd.)Rotorua3015New Zealand
| | - Eugenio Sanfuentes Von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de BiotecnologíaUniversidad de ConcepciónConcepción4070386Chile
| | - Mariela González
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de BiotecnologíaUniversidad de ConcepciónConcepción4070386Chile
| | - Rowena Hill
- Biosciences, University of ExeterStocker RoadExeterEX4 4QDUK
- Jodrell LaboratoryRoyal Botanic GardensKewTW9 3DSUK
| | | | - Murray Grant
- Biosciences, University of ExeterStocker RoadExeterEX4 4QDUK
- Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Nari M. Williams
- Scion (New Zealand Forest Research Institute, Ltd.)Rotorua3015New Zealand
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Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal. mSphere 2017; 2:mSphere00408-17. [PMID: 29202039 PMCID: PMC5700374 DOI: 10.1128/msphere.00408-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles-alveolate-Rhizaria (SAR) supergroup and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. This study investigated the expansion and evolution of effectors in 37 oomycete species in 4 oomycete orders, including Albuginales, Peronosporales, Pythiales, and Saprolegniales species. Our results highlight the large expansions of effector protein families, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, in Phytophthora species. Species-specific expansions, including expansions of chitinases in Aphanomyces astaci and Pythium oligandrum, were detected. Novel effectors which may be involved in suppressing animal immune responses in Ap. astaci and Py. insidiosum were also identified. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located in a number of oomycete species. We also investigated the "RxLR" effector complement of all 37 species and, as expected, observed large expansions in Phytophthora species numbers. Our results provide in-depth sequence information on all putative RxLR effectors from all 37 species. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. IMPORTANCE The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.
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10
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Longmuir AL, Beech PL, Richardson MF. Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi. F1000Res 2017; 6:1972. [PMID: 29188023 PMCID: PMC5698912 DOI: 10.12688/f1000research.12867.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 11/20/2022] Open
Abstract
Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The current reference genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, robust genome assemblies of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings: Some 308 million raw reads were generated for the two strains, DU054 and WA94.26. Independent genome assembly produced final genome sequences of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 94.4% and 91.5% of the stramenopile single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analyses and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.
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Affiliation(s)
- Amy L. Longmuir
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia
| | - Peter L. Beech
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia
| | - Mark F. Richardson
- Bioinformatics Core Research Group, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
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11
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Longmuir AL, Beech PL, Richardson MF. Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi. F1000Res 2017; 6:1972. [PMID: 29188023 PMCID: PMC5698912 DOI: 10.12688/f1000research.12867.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2017] [Indexed: 01/14/2023] Open
Abstract
Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings: Some 308 million raw reads were generated for the two strains. Independent genome assembly produced final genomes of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 82.5% and 81.8% of the eukaryote universal single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analysis and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.
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Affiliation(s)
- Amy L. Longmuir
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia
| | - Peter L. Beech
- Centre for Cellular and Molecular Biology, School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia
| | - Mark F. Richardson
- Bioinformatics Core Research Group, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
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12
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Turner J, O'Neill P, Grant M, Mumford RA, Thwaites R, Studholme DJ. Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum, a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants. GENOMICS DATA 2017; 12:17-21. [PMID: 28243575 PMCID: PMC5320048 DOI: 10.1016/j.gdata.2017.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/05/2017] [Indexed: 11/24/2022]
Abstract
Here we present genome sequences for twelve isolates of the invasive pathogen Phytophthora ramorum EU1. The assembled genome sequences and raw sequence data are available via BioProject accession number PRJNA177509. These data will be useful in developing molecular tools for specific detection and identification of this pathogen.
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Affiliation(s)
- Judith Turner
- Fera Science Ltd (Fera), National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Paul O'Neill
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Murray Grant
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Rick A. Mumford
- Fera Science Ltd (Fera), National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Richard Thwaites
- Fera Science Ltd (Fera), National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, United Kingdom
| | - David J. Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
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Grenville-Briggs LJ, Kushwaha SK, Cleary MR, Witzell J, Savenkov EI, Whisson SC, Chawade A, Vetukuri RR. Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech ( Fagus sylvatica). GENOMICS DATA 2017; 12:155-156. [PMID: 28560165 PMCID: PMC5435576 DOI: 10.1016/j.gdata.2017.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/06/2022]
Abstract
Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malmö, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81 Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000. The version described in this paper is version NBIJ01000000.
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Affiliation(s)
- Laura J Grenville-Briggs
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Sandeep K Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Department of Biology, Lund University, Lund, Sweden
| | - Michelle R Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Johanna Witzell
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eugene I Savenkov
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Stephen C Whisson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Gagnon MC, Feau N, Dale AL, Dhillon B, Hamelin RC, Brasier CM, Grünwald NJ, Brière SC, Bilodeau GJ. Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data. PLANT DISEASE 2017; 101:666-673. [PMID: 30678572 DOI: 10.1094/pdis-11-16-1586-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.
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Affiliation(s)
| | - Nicolas Feau
- Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Angela L Dale
- Faculty of Forestry, University of British Columbia (UBC), Vancouver, BC, Canada
| | - Braham Dhillon
- UBC and Department of Plant Pathology, University of Arkansas, Fayetteville
| | - Richard C Hamelin
- UBC and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes. mSphere 2017; 2:mSphere00095-17. [PMID: 28435885 PMCID: PMC5390094 DOI: 10.1128/msphere.00095-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022] Open
Abstract
The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the Phytophthora genus. The onset of next-generation sequencing techniques now means that a wealth of oomycete genomic data is available. For the first time, we have used genome-scale phylogenetic methods to resolve oomycete phylogenetic relationships. We used supertree methods to generate single-gene and multigene species phylogenies. Overall, our supertree analyses utilized phylogenetic data from 8,355 oomycete gene families. We have also complemented our analyses with superalignment phylogenies derived from 131 single-copy ubiquitous gene families. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and clades. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus. Genome-scale phylogenetic studies have successfully resolved many eukaryotic relationships by using supertree methods, which combine large numbers of potentially disparate trees to determine evolutionary relationships that cannot be inferred from individual phylogenies alone. With a sufficient amount of genomic data now available, we have undertaken the first whole-genome phylogenetic analysis of the oomycetes using data from 37 oomycete species and 6 SAR species. In our analysis, we used established supertree methods to generate phylogenies from 8,355 homologous oomycete and SAR gene families and have complemented those analyses with both phylogenomic network and concatenated supermatrix analyses. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and individual clades within the problematic Phytophthora genus. Support for the resolution of the inferred relationships between individual Phytophthora clades varies depending on the methodology used. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. IMPORTANCE The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the Phytophthora genus. The onset of next-generation sequencing techniques now means that a wealth of oomycete genomic data is available. For the first time, we have used genome-scale phylogenetic methods to resolve oomycete phylogenetic relationships. We used supertree methods to generate single-gene and multigene species phylogenies. Overall, our supertree analyses utilized phylogenetic data from 8,355 oomycete gene families. We have also complemented our analyses with superalignment phylogenies derived from 131 single-copy ubiquitous gene families. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and clades. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes.
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Ye W, Wang Y, Shen D, Li D, Pu T, Jiang Z, Zhang Z, Zheng X, Tyler BM, Wang Y. Sequencing of the Litchi Downy Blight Pathogen Reveals It Is a Phytophthora Species With Downy Mildew-Like Characteristics. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:573-83. [PMID: 27183038 DOI: 10.1094/mpmi-03-16-0056-r] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.
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Affiliation(s)
- Wenwu Ye
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Wang
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Delong Li
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianhuizi Pu
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zide Jiang
- 3 Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Zhengguang Zhang
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaobo Zheng
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Brett M Tyler
- 2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A.; and
| | - Yuanchao Wang
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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