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Shands AC, Xu G, Belisle RJ, Seifbarghi S, Jackson N, Bombarely A, Cano LM, Manosalva PM. Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles. Front Microbiol 2024; 15:1341803. [PMID: 39211322 PMCID: PMC11357935 DOI: 10.3389/fmicb.2024.1341803] [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: 11/20/2023] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140-141 Mb genomes with 21,111-21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana, and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility.
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Affiliation(s)
- Aidan C. Shands
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Guangyuan Xu
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Rodger J. Belisle
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Shirin Seifbarghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Natasha Jackson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valéncia, Valencia, Spain
| | - Liliana M. Cano
- Department of Plant Pathology, Indian River Research and Education Center (IRREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Fort Pierce, FL, United States
| | - Patricia M. Manosalva
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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Zhang J, Hieno A, Otsubo K, Feng W, Kageyama K. Population Genetic Analysis of Phytophthora colocasiae from Taro in Japan Using SSR Markers. J Fungi (Basel) 2023; 9:jof9040391. [PMID: 37108846 PMCID: PMC10145753 DOI: 10.3390/jof9040391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Phytophthora colocasiae is an important pathogen that causes great economic losses in taro production in tropical and subtropical regions, especially in Japan. Understanding the genetic variations in P. colocasiae populations and their transmission patterns in Japan is essential for effective disease control. Here, the genetic diversity of 358 P. colocasiae isolates, including 348 from Japan, 7 from China, and 3 from Indonesia, was assessed using 11 simple sequence repeat (SSR) primer pairs with high polymorphism. The phylogenetic tree of the SSR locus showed that the isolates from Japan could be divided into 14 groups, with group A being the dominant group. Among foreign isolates, only six from mainland China were similar to those from Japan and clustered in groups B and E. Analysis of molecular variance (AMOVA), principal components analysis (PCA), and cluster analysis (K = 3) results revealed a moderate level of genetic diversity, mainly within individuals. Populations showed high heterozygosity, a lack of regional differentiation, and frequent gene flow. Analysis of mating types and ploidy levels revealed that A2 and self-fertile (SF) A2 types and tetraploids were dominant across populations. Explanations and hypotheses for the results can provide more effective strategies for disease management of taro leaf blight.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kayoko Otsubo
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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Emergence of self-fertile Phytophthora colocasiae is a possible reason for the widespread expansion and persistence of taro leaf blight in Japan. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01762-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Masuda S, Yaeno T, Shibata H, Yorozu S, Yamamoto S, Shirasu K. High-Quality Genome Sequence Resource of the Taro Pathogen Phytophthora colocasiae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:297-299. [PMID: 35139662 DOI: 10.1094/mpmi-05-21-0120-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: 06/14/2023]
Affiliation(s)
- Sachiko Masuda
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Takashi Yaeno
- Department of Agriculture, Ehime University, Matsuyama, 790-8566, Japan
| | - Hideaki Shibata
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Matsuyama, 799-2405, Japan
| | - Shuuhei Yorozu
- Agriculture and Horticulture Division, Agriculture, Forestry and Fisheries Department, Ehime Prefectural Government, Matsuyama, 790-0001, Japan
| | - Satoki Yamamoto
- Agriculture and Horticulture Division, Agriculture, Forestry and Fisheries Department, Ehime Prefectural Government, Matsuyama, 790-0001, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
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Gerstein AC, Sharp NP. The population genetics of ploidy change in unicellular fungi. FEMS Microbiol Rev 2021; 45:6121427. [PMID: 33503232 DOI: 10.1093/femsre/fuab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
Changes in ploidy are a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.
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Affiliation(s)
- Aleeza C Gerstein
- Dept. of Microbiology, Dept. of Statistics, University of Manitoba Canada
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Vogel G, Gore MA, Smart CD. Genome-Wide Association Study in New York Phytophthora capsici Isolates Reveals Loci Involved in Mating Type and Mefenoxam Sensitivity. PHYTOPATHOLOGY 2021; 111:204-216. [PMID: 32539639 DOI: 10.1094/phyto-04-20-0112-fi] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phytophthora capsici is a soilborne oomycete plant pathogen that causes severe vegetable crop losses in New York (NY) state and worldwide. This pathogen is difficult to manage, in part due to its production of long-lasting sexual spores and its tendency to quickly evolve fungicide resistance. We single nucleotide polymorphism (SNP) genotyped 252 P. capsici isolates, predominantly from NY, in order to conduct a genome-wide association study for mating type and mefenoxam sensitivity. The population structure and extent of chromosomal copy number variation in this collection of isolates were also characterized. Population structure analyses showed isolates largely clustered by the field site where they were collected, with values of FST between pairs of fields ranging from 0.10 to 0.31. Thirty-three isolates were putative aneuploids, demonstrating evidence for having up to four linkage groups present in more than two copies, and an additional two isolates appeared to be genome-wide triploids. Mating type was mapped to a region on scaffold 4, consistent with previous findings, and mefenoxam sensitivity was associated with several SNP markers at a novel locus on scaffold 62. We identified several candidate genes for mefenoxam sensitivity, including a homolog of yeast ribosome synthesis factor Rrp5, but failed to locate near the scaffold 62 locus any subunits of RNA polymerase I, the hypothesized target site of phenylamide fungicides in oomycetes. This work expands our knowledge of the population biology of P. capsici and provides a foundation for functional validation of candidate genes associated with epidemiologically important phenotypes.
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Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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Vetukuri RR, Kushwaha SK, Sen D, Whisson SC, Lamour KH, Grenville-Briggs LJ. Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:903-905. [PMID: 29558317 DOI: 10.1094/mpmi-12-17-0321-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phytophthora colocasiae is a phytopathogenic oomycete that causes leaf blight and corm rot on taro (Colocasia esculenta), an important staple crop in the tropics. The impact of P. colocasiae is a serious concern for food security in Asian and Oceanic regions. Vietnamese strain 7290 of P. colocasiae was sequenced (Illumina) to assemble a draft genome of 56.6 Mb, comprised of 19,853 scaffolds and 19,984 predicted protein-coding genes. As in other Phytophthora species, P. colocasiae possesses numerous pathogenicity-related genes, such as the RxLR class of effectors. This draft genome sequence of P. colocasiae provides a resource to underpin the first steps in determining the molecular mechanisms of disease development in this pathosystem.
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Affiliation(s)
- Ramesh R Vetukuri
- 1 Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Stockholm Sweden
| | - Sandeep K Kushwaha
- 2 Department of Plant Breeding, Swedish University of Agricultural Sciences
| | - Diya Sen
- 1 Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Stockholm Sweden
| | - Stephen C Whisson
- 3 Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, U.K.; and
| | - Kurt H Lamour
- 4 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, U.S.A
| | - Laura J Grenville-Briggs
- 1 Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Stockholm Sweden
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Nawaz K, Shahid AA, Bengyella L, Subhani MN, Ali M, Anwar W, Iftikhar S, Ali SW. Evidence of genetically diverse virulent mating types of Phytophthora capsici from Capsicum annum L. World J Microbiol Biotechnol 2018; 34:130. [PMID: 30101403 DOI: 10.1007/s11274-018-2511-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/28/2018] [Indexed: 11/25/2022]
Abstract
Chili pepper (Capsicum annum L.) is an important economic crop that is severely destroyed by the filamentous oomycete Phytophthora capsici. Little is known about this pathogen in key chili pepper farms in Punjab province, Pakistan. We investigated the genetic diversity of P. capsici strains using standard taxonomic and molecular tools, and characterized their colony growth patterns as well as their disease severity on chili pepper plants under the greenhouse conditions. Phylogenetic analysis based on ribosomal DNA (rDNA), β-tubulin and translation elongation factor 1α loci revealed divergent evolution in the population structure of P. capsici isolates. The mean oospore diameter of mating type A1 isolates was greater than that of mating type A2 isolates. We provide first evidence of an uneven distribution of highly virulent mating type A1 and A2 of P. capsici that are insensitive to mefenoxam, pyrimorph, dimethomorph, and azoxystrobin fungicides, and represent a risk factor that could ease outpacing the current P. capsici management strategies.
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Affiliation(s)
- Kiran Nawaz
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan.
| | - Ahmad Ali Shahid
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Louis Bengyella
- Tree Fruit Research and Extension Center (TFREC), College of Agricultural, Human and Natural Resource Sciences (CAHNRS), Washington State University, Wenatchee, USA.
- Department of Biological Control, Advanced Biotech Cooperative, Bali-Nyonga, Cameroon.
| | | | - Muhammad Ali
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
| | - Waheed Anwar
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
| | - Sehrish Iftikhar
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
| | - Shinawar Waseem Ali
- Institute of Agricultural Science, University of the Punjab, Lahore, Pakistan
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Barchenger DW, Lamour KH, Bosland PW. Challenges and Strategies for Breeding Resistance in Capsicum annuum to the Multifarious Pathogen, Phytophthora capsici. FRONTIERS IN PLANT SCIENCE 2018; 9:628. [PMID: 29868083 PMCID: PMC5962783 DOI: 10.3389/fpls.2018.00628] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Phytophthora capsici is the most devastating pathogen for chile pepper production worldwide and current management strategies are not effective. The population structure of the pathogen is highly variable and few sources of widely applicable host resistance have been identified. Recent genomic advancements in the host and the pathogen provide important insights into the difficulties reported by epidemiological and physiological studies published over the past century. This review highlights important challenges unique to this complex pathosystem and suggests strategies for resistance breeding to help limit losses associated with P. capsici.
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Affiliation(s)
- Derek W. Barchenger
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Kurt H. Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
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10
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Genetic diversity of Phytophthora capsici recovered from Massachusetts between 1997 and 2014. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1334-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Barchenger DW, Lamour KH, Sheu ZM, Shrestha S, Kumar S, Lin SW, Burlakoti R, Bosland PW. Intra- and Intergenomic variation of Ploidy and Clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1330-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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