1
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Mandal K, Dutta S, Upadhyay A, Panda A, Tripathy S. Comparative Genome Analysis Across 128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution and Localized Evolution of Compartmentalized Genomes. Front Microbiol 2022; 13:806398. [PMID: 35369471 PMCID: PMC8967354 DOI: 10.3389/fmicb.2022.806398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of (TTTAGGG)n or (TTAGGGT)n rather than the canonical (TTAGGG)n. RxLR (arginine-any amino acid-leucine-arginine) motifs containing effectors diverge rapidly in Phytophthora and do not show any core common group. The RxLR effectors of some Phytophthora isolates have a tendency to form clusters with RxLRs from other species than within the same species. An analysis of the flanking intergenic distance clearly indicates a two-speed genome organization for all the Phytophthora isolates. Apart from effectors and the transposons, a large number of other virulence genes such as carbohydrate-active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP-binding cassette transporters (ABC), and ubiquitins are also present in the repeat-rich compartments. This indicates a rapid co-evolution of this powerful arsenal for successful pathogenicity. Whole genome duplication studies indicate that the pattern followed is more specific to a geographic location. To conclude, the large-scale genomic studies of Phytophthora have thrown light on their adaptive evolution, which is largely guided by the localized host-mediated selection pressure.
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Affiliation(s)
- Kajal Mandal
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Subhajeet Dutta
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Upadhyay
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Panda
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, United States
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Feng H, Ye W, Liu Z, Wang Y, Chen J, Wang Y, Zheng X. Development of LAMP Assays Using a Novel Target Gene for Specific Detection of Pythium terrestris, Pythium spinosum, and ' Candidatus Pythium huanghuaiense'. PLANT DISEASE 2021; 105:2888-2897. [PMID: 33823611 DOI: 10.1094/pdis-01-21-0068-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pythium terrestris, Pythium spinosum, and 'Candidatus Pythium huanghuaiense' are closely related species and important pathogens of soybean that cause root rot. However, the sequences of commonly used molecular markers, such as rDNA internal transcribed spacer 2 and cytochrome oxidase 1 gene, are similar among these species, making it difficult to design species-specific primers for loop-mediated isothermal amplification (LAMP) assays. The genome sequences of these species are also currently unavailable. Based on a comparative genomic analysis and de novo RNA-sequencing transcript assemblies, we identified and cloned the sequences of the M90 gene, a conserved but highly polymorphic single-copy gene encoding a Puf family RNA-binding protein among oomycetes. After primer design and screening, three LAMP assays were developed that specifically amplified the targeted DNA sequences in P. terrestris and P. spinosum at 62°C for 70 min and in 'Ca. Pythium huanghuaiense' at 62°C for 60 min. After adding SYBR Green I, a positive yellow-green color (under natural light) or intense green fluorescence (under ultraviolet light) was observed by the naked eye only in the presence of the target species. The minimum concentration of target DNA detected in all three LAMP assays was 100 pg·μl-1. The assays also successfully detected the target Pythium spp. with high accuracy and sensitivity from inoculated soybean seedlings and soils collected from soybean fields. This study provides a method for identification and cloning of candidate detection targets without a reference genome sequence and identified M90 as a novel specific target for molecular detection of three Pythium species causing soybean root rot.
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Affiliation(s)
- Hui Feng
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Zhuoyuan Liu
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Yang Wang
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Jiajia Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China
| | - Yuanchao Wang
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
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3
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Wang S, Xing R, Wang Y, Shu H, Fu S, Huang J, Paulus JK, Schuster M, Saunders DGO, Win J, Vleeshouwers V, Wang Y, Zheng X, van der Hoorn RAL, Dong S. Cleavage of a pathogen apoplastic protein by plant subtilases activates host immunity. THE NEW PHYTOLOGIST 2021; 229:3424-3439. [PMID: 33251609 DOI: 10.1111/nph.17120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
The plant apoplast is a harsh environment in which hydrolytic enzymes, especially proteases, accumulate during pathogen infection. However, the defense functions of most apoplastic proteases remain largely elusive. We show here that a newly identified small cysteine-rich secreted protein PC2 from the potato late blight pathogen Phytophthora infestans induces immunity in Solanum plants only after cleavage by plant apoplastic subtilisin-like proteases, such as tomato P69B. A minimal 61 amino acid core peptide carrying two key cysteines, conserved widely in most oomycete species, is sufficient for PC2-induced cell death. Furthermore, we showed that Kazal-like protease inhibitors, such as EPI1, produced by P. infestans prevent PC2 cleavage and dampen PC2 elicited host immunity. This study reveals that cleavage of pathogen proteins to release immunogenic peptides is an important function of plant apoplastic proteases.
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Affiliation(s)
- Shuaishuai Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongkang Xing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haidong Shu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shenggui Fu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Huang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Judith K Paulus
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Mariana Schuster
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Diane G O Saunders
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Vivianne Vleeshouwers
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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4
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Yin M, Zhang Z, Xuan M, Feng H, Ye W, Zheng X, Wang Y. Conserved Subgroups of the Plant-Specific RWP-RK Transcription Factor Family Are Present in Oomycete Pathogens. Front Microbiol 2020; 11:1724. [PMID: 32849368 PMCID: PMC7399023 DOI: 10.3389/fmicb.2020.01724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Nitrogen is a major constituent of proteins, chlorophyll, nucleotides, and hormones and has profound effects on plant growth and productivity. RWP-RK family transcription factors (TFs) are key regulators that bind to cis-acting elements in the promoter regions of nitrogen use efficiency-related genes and genes responsible for gametogenesis and embryogenesis. The proteins share a conserved RWPxRK motif; have been found in all vascular plants, green algae, and slime molds; and are considered to be a plant-specific TF family. In this study, we show that RWP-RK proteins are also widely present in the Stramenopila kingdom, particularly among the oomycetes, with 12-15 members per species. These proteins form three distinct phylogenetic subgroups, two of which are relatively closely related to the nodule inception (NIN)-like protein (NLP) or the RWP-RK domain protein (RKD) subfamilies of plant RWP-RK proteins. The donor for horizontal gene transfer of RWP-RK domains to slime molds is likely to have been among the Stramenopila, predating the divide between brown algae and oomycetes. The RWP-RK domain has secondary structures that are conserved across plants and oomycetes, but several amino acids that may affect DNA-binding affinity differ. The transcriptional activities of orthologous RWP-RK genes were found to be conserved in oomycetes. Our results demonstrate that RWP-RK family TF genes are present in the oomycetes and form specific subgroups with functions that are likely conserved. Our results provide new insights for further understanding the evolution and function of this TF family in specific eukaryotic organisms.
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Affiliation(s)
- Maozhu Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Mingrun Xuan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Hui Feng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
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5
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Abstract
The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of the biggest threats to global food security and natural ecosystems. Within the oomycete class are highly diverse species that infect a broad range of animals and plants. Some of the most destructive plant pathogens are oomycetes, such as Phytophthora infestans, the agent of potato late blight and the cause of the Irish famine. Recent years have seen a dramatic increase in the number of sequenced oomycete genomes. Here we review the latest developments in oomycete genomics and some of the important insights that have been gained. Coupled with proteomic and transcriptomic analyses, oomycete genome sequences have revealed tremendous insights into oomycete biology, evolution, genome organization, mechanisms of infection, and metabolism. We also present an updated phylogeny of the oomycete class using a phylogenomic approach based on the 65 oomycete genomes that are currently available.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland.
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6
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Rujirawat T, Patumcharoenpol P, Kittichotirat W, Krajaejun T. Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5525202. [PMID: 31260041 PMCID: PMC6601393 DOI: 10.1093/database/baz082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/01/2019] [Accepted: 05/29/2019] [Indexed: 11/14/2022]
Abstract
Oomycetes form a unique group of the fungal-like, aquatic, eukaryotic microorganisms. Lifestyle and pathogenicity of the oomycetes are diverse. Many pathogenic oomycetes affect a broad range of plants and cause enormous economic loss annually. Some pathogenic oomycetes cause destructive and deadly diseases in a variety of animals, including humans. No effective antimicrobial agent against the oomycetes is available. Genomic data of many oomycetes are currently available. Comparative analyses of the oomycete genomes must be performed to better understand the oomycete biology and virulence, as well as to identify conserved and biologically important proteins that are potential diagnostic and therapeutic targets of these organisms. However, a tool that facilitates comparative genomic studies of the oomycetes is lacking. Here, we described in detail the Oomycete Gene Table, which is an online user-friendly bioinformatic tool, designed to search, analyze, compare and visualize gene contents of 20 oomycetes in a customizable table. Genomic contents of other oomycete species, when available, can be added to the existing database. Some of the applications of the Oomycete Gene Table include investigations of phylogenomic relationships, as well as identifications of biologically important and pathogenesis-related genes of oomycetes. In summary, the Oomycete Gene Table is a simple and useful tool for comparative genomic analyses of oomycetes.
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Affiliation(s)
- Thidarat Rujirawat
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand.,Research Center, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand.,Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand
| | - Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Ngamwongwan Road, Jatujak District, Bangkok 10900, Thailand
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian Chai Thale Road, Bang Khun Thian District, Bangkok 10150, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bang Khun Thian Chai Thale Road, Bang Khun Thian District Bangkok 10150, Thailand
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Ratchathewi District, Bangkok 10400, Thailand
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7
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Malar C M, Yuzon JD, Panda A, Kasuga T, Tripathy S. Updated Assembly of Phytophthora ramorum pr102 Isolate Incorporating Long Reads from PacBio Sequencing. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1472-1474. [PMID: 31306082 DOI: 10.1094/mpmi-05-19-0147-a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65-Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.
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Affiliation(s)
- Mathu Malar C
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Jennifer David Yuzon
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
- USDA-ARS, Davis, CA, U.S.A
| | - Arijit Panda
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Takao Kasuga
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
- USDA-ARS, Davis, CA, U.S.A
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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8
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Malar C M, Yuzon JD, Das S, Das A, Panda A, Ghosh S, Tyler BM, Kasuga T, Tripathy S. Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1047-1060. [PMID: 30794480 DOI: 10.1094/mpmi-08-18-0222-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.
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Affiliation(s)
- Mathu Malar C
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jennifer D Yuzon
- 3Department of Plant Pathology, University of California, Davis, CA, U.S.A
- 4USDA-ARS, Davis, CA, U.S.A
| | - Subhadeep Das
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhishek Das
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Arijit Panda
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samrat Ghosh
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Brett M Tyler
- 5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303, U.S.A
| | - Takao Kasuga
- 3Department of Plant Pathology, University of California, Davis, CA, U.S.A
- 4USDA-ARS, Davis, CA, U.S.A
| | - Sucheta Tripathy
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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9
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Panda A, Chaudhari NM, Mukherjee M, Ghosh S, Sarangi AN, Mathu Malar C, Kant S, Sen D, Das A, Das S, Singh D, Prusty A, Tripathy S. Genome/transcriptome collection of plethora of economically important, previously unexplored organisms from India and abroad. Data Brief 2019; 25:104099. [PMID: 31294057 PMCID: PMC6595405 DOI: 10.1016/j.dib.2019.104099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 11/24/2022] Open
Abstract
Genome and transcriptome sequencing data are extremely useful resources for researchers in carrying out biological experiments that involves cloning and characterizing genes. We are presenting here genome sequence data from different clades of life including photosynthetic prokaryotes; oomycetes pathogens; probiotic bacteria; endophytic yeasts and filamentous fungus and pathogenic protozoa Leishmania donovani. In addition, we are also presenting paired control and treated stress response transcriptomes of Cyanobacteria growing in extreme conditions. The Cyanobacterial species that are included in this dataset were isolated from extreme conditions including desiccated monuments, hot springs and saline archipelagos. The probiotic Lactobacillus paracasei was isolated from Indian sub-continent. The Kala azar causing protozoan Leishmania donovani, whose early infectious stage is also included in this dataset. The endophyte Arthrinium malaysianum was isolated as a contaminant has significant bio-remediation property. Our collaborators have isolated endophyte Rhodotorula mucilaginosa JGTA1 from Jaduguda mines, West Bengal, India infested with Uranium. Our collaborators have isolated a heterozygous diploid oomycetes pathogen, Phytophthora ramorum causing sudden oak death in CA, USA coast is also part of the data. These dataset presents a unique heterogeneous collection from various sources that are analyzed using “Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization” (Panda et al., 2019) and are presented in a web site automatically created by GAL at http://www.eumicrobedb.org/cglab.
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Affiliation(s)
- Arijit Panda
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Narendrakumar M Chaudhari
- Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Mayuri Mukherjee
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Samrat Ghosh
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Aditya Narayan Sarangi
- Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - C Mathu Malar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Shashi Kant
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Diya Sen
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Abhishek Das
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhadeep Das
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Deeksha Singh
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Asharani Prusty
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sucheta Tripathy
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.,Structural Biology and Bioinformatics Division Department, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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10
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Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution. PLoS Pathog 2019; 15:e1007729. [PMID: 31002734 PMCID: PMC6493774 DOI: 10.1371/journal.ppat.1007729] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/01/2019] [Accepted: 03/25/2019] [Indexed: 12/12/2022] Open
Abstract
The use of host nutrients to support pathogen growth is central to disease. We addressed the relationship between metabolism and trophic behavior by comparing metabolic gene expression during potato tuber colonization by two oomycetes, the hemibiotroph Phytophthora infestans and the necrotroph Pythium ultimum. Genes for several pathways including amino acid, nucleotide, and cofactor biosynthesis were expressed more by Ph. infestans during its biotrophic stage compared to Py. ultimum. In contrast, Py. ultimum had higher expression of genes for metabolizing compounds that are normally sequestered within plant cells but released to the pathogen upon plant cell lysis, such as starch and triacylglycerides. The transcription pattern of metabolic genes in Ph. infestans during late infection became more like that of Py. ultimum, consistent with the former's transition to necrotrophy. Interspecific variation in metabolic gene content was limited but included the presence of γ-amylase only in Py. ultimum. The pathogens were also found to employ strikingly distinct strategies for using nitrate. Measurements of mRNA, 15N labeling studies, enzyme assays, and immunoblotting indicated that the assimilation pathway in Ph. infestans was nitrate-insensitive but induced during amino acid and ammonium starvation. In contrast, the pathway was nitrate-induced but not amino acid-repressed in Py. ultimum. The lack of amino acid repression in Py. ultimum appears due to the absence of a transcription factor common to fungi and Phytophthora that acts as a nitrogen metabolite repressor. Evidence for functional diversification in nitrate reductase protein was also observed. Its temperature optimum was adapted to each organism's growth range, and its Km was much lower in Py. ultimum. In summary, we observed divergence in patterns of gene expression, gene content, and enzyme function which contribute to the fitness of each species in its niche. A key feature of disease is the pathogen's consumption of host metabolites to support its growth and multiplication. Understanding how host nutrients are used by pathogens may lead to strategies for limiting disease, for example by developing inhibitors of metabolic pathways needed for pathogen growth. Feeding strategies of plant pathogens range between two extremes: necrotrophs kill host cells and consume the released nutrients, while biotrophs do not injure host cells but instead acquire nutrients from extracellular spaces in the plant. In this study, a comparison was made between the metabolism of Phytophthora infestans (the infamous Irish Famine pathogen) and Pythium ultimum during potato tuber colonization. These microbes have close evolutionary histories, but while Py. ultimum is a necrotroph, Ph. infestans is a biotroph for most of the disease cycle. It was discovered that distinct patterns of metabolic gene expression, gene content, and enzyme behavior underlie these lifestyles. For example, genes for utilizing compounds that are normally stored within plant cells were expressed more by Py. ultimum, while Ph. infestans appeared to synthesize more biosubstances from precursors. Several differences in carbon and nitrogen metabolism were linked to variation in enzyme content and gene expression regulators in the two species.
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11
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McGowan J, Byrne KP, Fitzpatrick DA. Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). Genome Biol Evol 2019; 11:189-206. [PMID: 30535146 PMCID: PMC6330052 DOI: 10.1093/gbe/evy267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 01/01/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles–alveolates–rhizaria eukaryotic supergroup. They include some of the most destructive pathogens of animals and plants, such as Phytophthora infestans, the causative agent of late potato blight. Despite the threat they pose to worldwide food security and natural ecosystems, there is a lack of tools and databases available to study oomycete genetics and evolution. To this end, we have developed the Oomycete Gene Order Browser (OGOB), a curated database that facilitates comparative genomic and syntenic analyses of oomycete species. OGOB incorporates genomic data for 20 oomycete species including functional annotations and a number of bioinformatics tools. OGOB hosts a robust set of orthologous oomycete genes for evolutionary analyses. Here, we present the structure and function of OGOB as well as a number of comparative genomic analyses we have performed to better understand oomycete genome evolution. We analyze the extent of oomycete gene duplication and identify tandem gene duplication as a driving force of the expansion of secreted oomycete genes. We identify core genes that are present and microsyntenically conserved (termed syntenologs) in oomycete lineages and identify the degree of microsynteny between each pair of the 20 species housed in OGOB. Consistent with previous comparative synteny analyses between a small number of oomycete species, our results reveal an extensive degree of microsyntenic conservation amongst genes with housekeeping functions within the oomycetes. OGOB is available at https://ogob.ie.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Co. Kildare, Ireland.,Human Health Research Institute, Maynooth University, Co. Kildare, Ireland
| | - Kevin P Byrne
- School of Medicine, UCD Conway Institute, University College Dublin, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Co. Kildare, Ireland.,Human Health Research Institute, Maynooth University, Co. Kildare, Ireland
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12
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Vetukuri RR, Tripathy S, Malar C M, Panda A, Kushwaha SK, Chawade A, Andreasson E, Grenville-Briggs LJ, Whisson SC. Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora. Genome Biol Evol 2018; 10:2432-2442. [PMID: 30060094 PMCID: PMC6152947 DOI: 10.1093/gbe/evy162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/19/2022] Open
Abstract
Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.
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Affiliation(s)
- Ramesh R Vetukuri
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Mathu Malar C
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Arijit Panda
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Sandeep K Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Department of Biology, Lund University, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Laura J Grenville-Briggs
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Stephen C Whisson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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13
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Elliott M, Yuzon J, C MM, Tripathy S, Bui M, Chastagner GA, Coats K, Rizzo DM, Garbelotto M, Kasuga T. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics 2018; 19:320. [PMID: 29720102 PMCID: PMC5932867 DOI: 10.1186/s12864-018-4709-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accumulating evidence suggests that genome plasticity allows filamentous plant pathogens to adapt to changing environments. Recently, the generalist plant pathogen Phytophthora ramorum has been documented to undergo irreversible phenotypic alterations accompanied by chromosomal aberrations when infecting trunks of mature oak trees (genus Quercus). In contrast, genomes and phenotypes of the pathogen derived from the foliage of California bay (Umbellularia californica) are usually stable. We define this phenomenon as host-induced phenotypic diversification (HIPD). P. ramorum also causes a severe foliar blight in some ornamental plants such as Rhododendron spp. and Viburnum spp., and isolates from these hosts occasionally show phenotypes resembling those from oak trunks that carry chromosomal aberrations. The aim of this study was to investigate variations in phenotypes and genomes of P. ramorum isolates from non-oak hosts and substrates to determine whether HIPD changes may be equivalent to those among isolates from oaks. RESULTS We analyzed genomes of diverse non-oak isolates including those taken from foliage of Rhododendron and other ornamental plants, as well as from natural host species, soil, and water. Isolates recovered from artificially inoculated oak logs were also examined. We identified diverse chromosomal aberrations including copy neutral loss of heterozygosity (cnLOH) and aneuploidy in isolates from non-oak hosts. Most identified aberrations in non-oak hosts were also common among oak isolates; however, trisomy, a frequent type of chromosomal aberration in oak isolates was not observed in isolates from Rhododendron. CONCLUSION This work cross-examined phenotypic variation and chromosomal aberrations in P. ramorum isolates from oak and non-oak hosts and substrates. The results suggest that HIPD comparable to that occurring in oak hosts occurs in non-oak environments such as in Rhododendron leaves. Rhododendron leaves are more easily available than mature oak stems and thus can potentially serve as a model host for the investigation of HIPD, the newly described plant-pathogen interaction.
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Affiliation(s)
- Marianne Elliott
- Washington State University Puyallup Research and Extension Center, Puyallup, Washington, 98371, USA
| | - Jennifer Yuzon
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Mathu Malar C
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
| | - Mai Bui
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, 95616, USA
| | - Gary A Chastagner
- Washington State University Puyallup Research and Extension Center, Puyallup, Washington, 98371, USA
| | - Katie Coats
- Washington State University Puyallup Research and Extension Center, Puyallup, Washington, 98371, USA
| | - David M Rizzo
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Matteo Garbelotto
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, 94720, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, 95616, USA.
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14
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Abstract
The population structure of the Phytophthora infestans populations that caused the recent 2013–14 late blight epidemic in eastern India (EI) and northeastern India (NEI) was examined. The data provide new baseline information for populations of P. infestans in India. A migrant European 13_A2 genotype was responsible for the 2013–14 epidemic, replacing the existing populations. Mutations have generated substantial sub-clonal variation with 24 multi-locus genotypes (MLGs) found, of which 19 were unique variants not yet reported elsewhere globally. Samples from West Bengal were the most diverse and grouped alongside MLGs found in Europe, the UK and from neighbouring Bangladesh but were not linked directly to most samples from south India. The pathogen population was broadly more aggressive on potato than on tomato and resistant to the fungicide metalaxyl. Pathogen population diversity was higher in regions around the international borders with Bangladesh and Nepal. Overall, the multiple shared MLGs suggested genetic contributions from UK and Europe in addition to a sub-structure based on the geographical location within India. Our data indicate the need for improved phytosanitary procedures and continuous surveillance to prevent the further introduction of aggressive lineages of P. infestans into the country.
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15
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Ah-Fong AMV, Kagda M, Judelson HS. Illuminating Phytophthora Biology with Fluorescent Protein Tags. Methods Mol Biol 2018; 1848:119-129. [PMID: 30182233 DOI: 10.1007/978-1-4939-8724-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phytophthora species cause diseases that threaten agricultural, ornamental, and forest plants worldwide. Explorations of the biology of these pathogens have been aided by the availability of genome sequences, but much work remains to decipher the roles of their proteins. Insight into protein function can be obtained by visualizing them within cells, which has been facilitated by recent improvements in fluorescent protein and microscope technologies. Here, we describe strategies to permit investigators to generate strains of Phytophthora that express fluorescently tagged proteins and study their localization during growth in artificial media and during plant infection.
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Affiliation(s)
- Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Meenakshi Kagda
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
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