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Wu Y, Zhang B, Liu S, Zhao Z, Ren W, Chen L, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Han F, Zhang Y. A Whole-Genome Assembly for Hyaloperonospora parasitica, A Pathogen Causing Downy Mildew in Cabbage ( Brassica oleracea var. capitata L.). J Fungi (Basel) 2023; 9:819. [PMID: 37623590 PMCID: PMC10456066 DOI: 10.3390/jof9080819] [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: 05/25/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Hyaloperonospora parasitica is a global pathogen that can cause leaf necrosis and seedling death, severely threatening the quality and yield of cabbage. However, the genome sequence and infection mechanisms of H. parasitica are still unclear. Here, we present the first whole-genome sequence of H. parasitica isolate BJ2020, which causes downy mildew in cabbage. The genome contains 4631 contigs and 9991 protein-coding genes, with a size of 37.10 Mb. The function of 6128 genes has been annotated. We annotated the genome of H. parasitica strain BJ2020 using databases, identifying 2249 PHI-associated genes, 1538 membrane transport proteins, and 126 CAZy-related genes. Comparative analyses between H. parasitica, H.arabidopsidis, and H. brassicae revealed dramatic differences among these three Brassicaceae downy mildew pathogenic fungi. Comprehensive genome-wide clustering analysis of 20 downy mildew-causing pathogens, which infect diverse crops, elucidates the closest phylogenetic affinity between H. parasitica and H. brassicae, the causative agent of downy mildew in Brassica napus. These findings provide important insights into the pathogenic mechanisms and a robust foundation for further investigations into the pathogenesis of H. parasitica BJ2020.
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Affiliation(s)
- Yuankang Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Bin Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Shaobo Liu
- China Vegetable Biotechnology (Shouguang) Co., Ltd., Shouguang 262700, China; (S.L.); (Z.Z.)
| | - Zhiwei Zhao
- China Vegetable Biotechnology (Shouguang) Co., Ltd., Shouguang 262700, China; (S.L.); (Z.Z.)
| | - Wenjing Ren
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Li Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Fengqing Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.W.); (B.Z.); (W.R.); (L.C.); (L.Y.); (M.Z.); (H.L.); (Y.W.); (J.J.)
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Chen X, Hao X, Akhberdi O, Zhu X. Genomic and Transcriptomic Survey Provides Insights into Molecular Basis of Pathogenicity of the Sunflower Pathogen Phoma macdonaldii. J Fungi (Basel) 2023; 9:jof9050520. [PMID: 37233231 DOI: 10.3390/jof9050520] [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: 03/13/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Phoma macdonaldii (teleomorph Leptosphaeria lindquistii) is the causal agent of sunflower (Helianthus annuus L.) black stem. In order to investigate the molecular basis for the pathogenicity of P. ormacdonaldii, genomic and transcriptomic analyses were performed. The genome size was 38.24 Mb and assembled into 27 contigs with 11,094 putative predicted genes. These include 1133 genes for CAZymes specific for plant polysaccharide degradation, 2356 for the interaction between the pathogen and host, 2167 for virulence factors, and 37 secondary metabolites gene clusters. RNA-seq analysis was conducted at the early and late stages of the fungal spot formation in infected sunflower tissues. A total of 2506, 3035, and 2660 differentially expressed genes (DEGs) between CT and each treatment group (LEAF-2d, LEAF-6d, and STEM) were retrieved, respectively. The most significant pathways of DEGs from these diseased sunflower tissues were the metabolic pathways and biosynthesis of secondary metabolites. Overall, 371 up-regulated DEGs were shared among LEAF-2d, LEAF-6d, and STEM, including 82 mapped to DFVF, 63 mapped to PHI-base, 69 annotated as CAZymes, 33 annotated as transporters, 91 annotated as secretory proteins, and a carbon skeleton biosynthetic gene. The most important DEGs were further confirmed by RT-qPCR. This is the first report on the genome-scale assembly and annotation for P. macdonaldii. Our data provide a framework for further revealing the underlying mechanism of the pathogenesis of P. macdonaldii, and also suggest the potential targets for the diseases caused by this fungal pathogen.
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Affiliation(s)
- Xuejing Chen
- College of Biological and Geography Sciences, Yili Normal University, Yining 835000, China
| | - Xiaoran Hao
- National Experimental Teaching Demonstrating Center, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Oren Akhberdi
- Key Laboratory of Microbial Resources Protection, Development and Utilization, Yili Normal University, Yining 835000, China
| | - Xudong Zhu
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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Qi LL, Talukder ZI, Ma GJ, Seiler GJ. Introgression and targeting of the Pl 37 and Pl 38 genes for downy mildew resistance from wild Helianthus annuus and H. praecox into cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:82. [PMID: 36952051 DOI: 10.1007/s00122-023-04316-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Two new downy mildew resistance genes, Pl37 and Pl38, were introgressed from wild sunflower species into cultivated sunflower and mapped to sunflower chromosomes 4 and 2, respectively Downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii (Farl.) Berl. & de Toni, is known as the most prevalent disease occurring in global sunflower production areas, especially in North America and Europe. In this study, we report the introgression and molecular mapping of two new DM resistance genes from wild sunflower species, Helianthus annuus and H. praecox, into cultivated sunflower. Two mapping populations were developed from the crosses of HA 89/H. annuus PI 435417 (Pop1) and CMS HA 89/H. praecox PRA-417 (Pop2). The phenotypic evaluation of DM resistance/susceptibility was conducted in the BC1F2-derived BC1F3 populations using P. halstedii race 734. The BC1F2 segregating Pop1 was genotyped using an Optimal GBS AgriSeq™ Panel consisting of 768 mapped SNP markers, while the BC1F2 segregating Pop2 was genotyped using a genotyping-by-sequencing approach. Linkage analysis and subsequent saturation mapping placed the DM resistance gene, designated Pl37, derived from H. annuus PI 435417 in a 1.6 cM genetic interval on sunflower chromosome 4. Pl37 co-segregated with SNP markers SPB0003 and C4_5738736. Similarly, linkage analysis and subsequent saturation mapping placed the DM resistance gene, designated Pl38, derived from H. praecox PRA-417 in a 0.8 cM genetic interval on sunflower chromosome 2. Pl38 co-segregated with seven SNP markers. Multi-pathotype tests revealed that lines with Pl37 or Pl38 are immune to the most prevalent and virulent P. halstedii races tested. Two germplasm lines, HA-DM15 with Pl37 and HA-DM16 with Pl38, were developed for use in sunflower DM-resistance breeding.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - Z I Talukder
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
| | - G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Ball Horticultural Company, 622 Town Road, West Chicago, IL, 60185, USA
| | - G J Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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Tör M, Wood T, Webb A, Göl D, McDowell JM. Recent developments in plant-downy mildew interactions. Semin Cell Dev Biol 2023; 148-149:42-50. [PMID: 36670035 DOI: 10.1016/j.semcdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/20/2023]
Abstract
Downy mildews are obligate oomycete pathogens that attack a wide range of plants and can cause significant economic impacts on commercial crops and ornamental plants. Traditionally, downy mildew disease control relied on an integrated strategies, that incorporate cultural practices, deployment of resistant cultivars, crop rotation, application of contact and systemic pesticides, and biopesticides. Recent advances in genomics provided data that significantly advanced understanding of downy mildew evolution, taxonomy and classification. In addition, downy mildew genomics also revealed that these obligate oomycetes have reduced numbers of virulence factor genes in comparison to hemibiotrophic and necrotrophic oomycetes. However, downy mildews do deploy significant arrays of virulence proteins, including so-called RXLR proteins that promote virulence or are recognized as avirulence factors. Pathogenomics are being applied to downy mildew population studies to determine the genetic diversity within the downy mildew populations and manage disease by selection of appropriate varieties and management strategies. Genome editing technologies have been used to manipulate host disease susceptibility genes in different plants including grapevine and sweet basil and thereby provide new soucres of resistance genes against downy mildews. Previously, it has proved difficult to transform and manipulate downy mildews because of their obligate lifestyle. However, recent exploitation of RNA interference machinery through Host-Induced Gene Silencing (HIGS) and Spray-Induced Gene Silencing (SIGS) indicate that functional genomics in downy mildews is now possible. Altogether, these breakthrough technologies and attendant fundamental understanding will advance our ability to mitigate downy mildew diseases.
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Affiliation(s)
- Mahmut Tör
- Department of Biology, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK.
| | | | | | - Deniz Göl
- Department of Biology, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
| | - John M McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061-0329, USA
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Buerstmayr H, Dreccer MF, Miladinović D, Qiu L, Rajcan I, Reif J, Varshney RK, Vollmann J. Plant breeding for increased sustainability: challenges, opportunities and progress. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3679-3683. [PMID: 36355071 DOI: 10.1007/s00122-022-04238-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Hermann Buerstmayr
- University of Natural Resources and Life Sciences Vienna, Vienna, Austria.
| | - Maria Fernanda Dreccer
- Commonwealth Scientific and Industrial Research Organisation - Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Lijuan Qiu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Jochen Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Stadt Seeland, Germany
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Johann Vollmann
- University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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Spatial Genetic Structure and Pathogenic Race Composition at the Field Scale in the Sunflower Downy Mildew Pathogen, Plasmopara halstedii. J Fungi (Basel) 2022; 8:jof8101084. [PMID: 36294648 PMCID: PMC9605284 DOI: 10.3390/jof8101084] [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: 06/22/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Yield losses in sunflower crops caused by Plasmopara halstedii can be up to 100%, depending on the cultivar susceptibility, environmental conditions, and virulence of the pathogen population. The aim of this study was to investigate the genetic and phenotypic structure of a sunflower downy mildew agent at the field scale. The genetic diversity of 250 P. halstedii isolates collected from one field in southern France was assessed using single-nucleotide polymorphisms (SNPs) and single sequence repeats (SSR). A total of 109 multilocus genotypes (MLG) were identified among the 250 isolates collected in the field. Four genotypes were repeated more than 20 times and spatially spread over the field. Estimates of genetic relationships among P. halstedii isolates using principal component analysis and a Bayesian clustering approach demonstrated that the isolates are grouped into two main genetic clusters. A high level of genetic differentiation among clusters was detected (FST = 0.35), indicating overall limited exchange between them, but our results also suggest that recombination between individuals of these groups is not rare. Genetic clusters were highly related to pathotypes, as previously described for this pathogen species. Eight different races were identified (100, 300, 304, 307, 703, 704, 707, and 714), with race 304 being predominant and present at most of the sites. The co-existence of multiple races at the field level is a new finding that could have important implications for the management of sunflower downy mildew. These data provide the first population-wide picture of the genetic structure of P. halstedii at a fine spatial scale.
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