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An In Silico Outlook for the Detection and Surveillance of Evolving and Persistent Plant Pathogens

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Detection, Diagnosis and Management of Soil-borne Phytopathogens

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Abstract

The diversity and social behaviour of plants are astounding. They developed a wide variety of molecular mechanisms to react to a complex network of environmental signals, multiple pathways activated by various responsive genes, abiotic stresses, and diseases brought on by bacteria, fungus, nematodes, and viruses that affect plant growth and crop yield. The molecular foundation of plant responses has thus been the subject of substantial research. The advancing omics technologies offer vital tactics for fostering molecular research and cutting-edge methods for omics-assisted crop improvement. Bioinformatics has aided in genome sequencing of various plant species, gene identification, phylogenetic profiling of plant species, detection of transcription factor binding sites of the genes, and the discovery of different sites where protein interactions can take place. To help to understand biology at the system level, bioinformatics begins to show promise in unravelling genetic networks. Plant life plays important and diverse roles in our society, our economy, and our global environment. Feeding the increasing world population is a challenge for the modern plant biotechnology. Crop yields have increased during the last century and will continue to improve by novel strategies and technologies. The transition from expressed sequence tags and microarray-based techniques to more potent strategies like RNA sequencing and related technologies has been encouraged by the next-generation sequencing, which has largely favoured deeper insights in plant genome organizations and on-functional responses to variable environmental parameters. Simultaneously, the development in the proteomics techniques that is 2D gel coupled to mass spectrometry, of high-throughput shotgun approaches, and of more robust LC-MS and GC-MS and metabonomic technologies are able to unravel fluctuations of non-volatiles and volatiles, paving the way to a better understanding of the effects of plant biological processes and investigations.

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References

  • Akinyemi IA, Wang F, Zhou B, Qi S, Wu Q (2016) Ecogenomic survey of plant viruses infecting tobacco by next generation sequencing. Virol J 13(1):1–12

    Article  Google Scholar 

  • Amara J, Bouaziz B, Algergawy A (2017) A deep learning-based approach for banana leaf diseases classification. Datenbanksysteme für Business, Technologie und Web (BTW 2017)-Workshopband

    Google Scholar 

  • Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J (2016) High throughput sequencing: an overview of sequencing chemistry. Indian J Microbiol 56(4):394–404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baker CJ, Stavely JR, Mock N (1985) Biocontrol of bean rust by Bacillus subtilis under field conditions. Plant Dis 69(9):770–772

    Google Scholar 

  • Balvočiūtė M, Huson DH, Silva R, Greengenes NCBI, OTT (2017) How do these taxonomies compare. BMC Genomics 18:114

    Article  PubMed  PubMed Central  Google Scholar 

  • Barbulovic-Nad I, Lucente M, Sun Y, Zhang M, Wheeler AR, Bussmann M (2006) Bio-microarray fabrication techniques—a review. Crit Rev Biotechnol 26(4):237–259

    Article  CAS  PubMed  Google Scholar 

  • Bartsch C, Höper D, Mäde D, Johne R (2018) Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR. Food Microbiol 76:390–395

    Article  CAS  PubMed  Google Scholar 

  • Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palù G (2013) Next-generation sequencing technologies in diagnostic virology. J Clin Virol 58(2):346–350

    Article  CAS  PubMed  Google Scholar 

  • Bevan MW, Uauy C, Wulff BBH, Zhou J, Krasileva K, Clark MD (2017) Genomic innovation for crop improvement. Nature 543:346–354

    Article  CAS  PubMed  Google Scholar 

  • Bhardwaj A, Kulshrestha S (2020) Advance methods for the isolation and characterization of plant viruses infecting crops. In: Awasthi LP (ed) Applied plant virology. Academic Press, Cambridge, MA, pp 39–53

    Chapter  Google Scholar 

  • Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5(7):566–582

    Article  CAS  PubMed  Google Scholar 

  • Bonfig KB, Schreiber U, Gabler A, Roitsch T, Berger S (2006) Infection with virulent and avirulent P. syringae strains differentially affects photosynthesis and sink metabolism in Arabidopsis leaves. Planta 225(1):1–12

    Article  CAS  PubMed  Google Scholar 

  • Bronzato Badial A, Sherman D, Stone A, Gopakumar A, Wilson V, Schneider W, King J (2018) Nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues. Plant Dis 102(8):1648–1652

    Article  PubMed  Google Scholar 

  • Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, McHardy AC, Schulze-Lefert P (2015) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17(3):392–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bumgarner R (2013) Overview of DNA microarrays: types, applications, and their future. Curr Protoc Mol Biol 101(1):22–31

    Article  Google Scholar 

  • Call DR (2005) Challenges and opportunities for pathogen detection using DNA microarrays. Crit Rev Microbiol 31(2):91–99

    Article  CAS  PubMed  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6(8):1621–1624. https://doi.org/10.1038/ismej.2012.8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chalupowicz L, Dombrovsky A, Gaba V, Luria N, Reuven M, Beerman A, Lachman O, Dror O, Nissan G, Manulis-Sasson S (2019) Diagnosis of plant diseases using the Nanopore sequencing platform. Plant Pathol 68(2):229–238

    Article  CAS  Google Scholar 

  • Chou CC, Lee TT, Chen CH, Hsiao HY, Lin YL, Ho MS, Yang PC, Peck K (2006) Design of microarray probes for virus identification and detection of emerging viruses at the genus level. BMC Bioinform 7(1):1–12

    Article  Google Scholar 

  • Dangl JL, Jones JD (2001) Plant pathogens and integrated defence responses to infection. Nature 411(6839):826–833

    Article  CAS  PubMed  Google Scholar 

  • Della Bartola M, Byrne S, Mullins E (2020) Characterization of potato virus Y isolates and assessment of nanopore sequencing to detect and genotype potato viruses. Viruses 12(4):478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dodds PN (2010) Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11(8):53948

    Article  Google Scholar 

  • Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MG (2020) PICRUSt2: an improved and customizable approach for metagenome inference. BioRxiv. https://doi.org/10.1101/672295

  • Duarte MF, Fonseca ME, Boiteux LS, Costa H, Ribeiro BM, Melo FL, Pereira-Carvalho RC (2020) Identification of Physalis angulata (Solanaceae) as a natural alternative weed host of tomato severe rugose virus in Brazil. Plant Dis 104:600. https://doi.org/10.1094/PDIS-07-19-1389-PDN

    Article  Google Scholar 

  • Egeland RD, Southern EM (2005) Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication. Nucleic Acids Res 33(14):e125–e125

    Article  PubMed  PubMed Central  Google Scholar 

  • Fellers JP, Webb C, Fellers MC, Shoup Rupp J, De Wolf E (2019) Wheat virus identification within infected tissue using nanopore sequencing technology. Plant Dis 103(9):2199–2203

    Article  CAS  PubMed  Google Scholar 

  • Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269(5223):496–512

    Article  CAS  PubMed  Google Scholar 

  • Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C (2018) Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods 15(11):962–968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garalde DR, Snell EA, Jachimowicz D, Sipos B, Lloyd JH, Bruce M, Pantic N, Admassu T, James P, Warland A, Jordan M (2018) Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods 15(3):201–206

    Article  CAS  PubMed  Google Scholar 

  • Ge B, Li Q, Liu G, Lu M, Li S, Wang H (2013) Simultaneous detection and identification of four viruses infecting Pepino by multiplex RT-PCR. Arch Virol 158(6):1181–1187

    Article  CAS  PubMed  Google Scholar 

  • Gilbert RJ, Bayley H, Anderluh G (2017) Membrane pores: from structure and assembly, to medicine and technology. Philos Trans R Soc Lond B Biol Sci 372:20160208

    Article  PubMed  PubMed Central  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis R, Dujon B, Feldmann H (1996) Life with 6000 genes. Science 274(5287):546–567. https://doi.org/10.1126/science.274.5287.546

    Article  CAS  PubMed  Google Scholar 

  • Goswami M, Akhtar S, Osama K (2018) Strategies for monitoring and modeling the growth of hairy root cultures: an in silico perspective. In: Hairy roots. Springer, Singapore, pp 311–327

    Chapter  Google Scholar 

  • Hadidi A (2019) Next-generation sequencing and CRISPR/Cas13 editing in viroid research and molecular diagnostics. Viruses 11(2):120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han T, Melvin CD, Shi L, Branham WS, Moland CL, Pine PS, Thompson KL, Fuscoe JC (2006) September. Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions. BMC Bioinform 7(2):1–13

    Google Scholar 

  • Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107(1):1–8

    Article  CAS  PubMed  Google Scholar 

  • Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29(3):548–562

    Article  CAS  PubMed  Google Scholar 

  • Hilbert DW, Ostendorf B (2001) The utility of artificial neural networks for modelling the distribution of vegetation in past, present and future climates. Ecol Model 146(1–3):311–327

    Article  Google Scholar 

  • Hoen PA, de Kort F, Van Ommen GJB, den Dunnen JT (2003) Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Res 31(5):e20–e20

    Article  PubMed  PubMed Central  Google Scholar 

  • Hu Y, Green GS, Milgate AW, Stone EA, Rathjen JP, Schwessinger B (2019) Pathogen detection and microbiome analysis of infected wheat using a portable DNA sequencer. Phytobiomes J 3(2):92–101

    Article  CAS  Google Scholar 

  • Huda S, Miah S, Hassan MM, Islam R, Yearwood J, Alrubaian M, Almogren A (2017) Defending unknown attacks on cyber-physical systems by semi-supervised approach and available unlabeled data. Inform Sci 379:211–228

    Article  Google Scholar 

  • Jagga Z, Gupta D (2014) Supervised learning classification models for prediction of plant virus encoded RNA silencing suppressors. PLoS One 9(5):e97446

    Article  PubMed  PubMed Central  Google Scholar 

  • Johnson SS, Zaikova E, Goerlitz DS, Bai Y, Tighe SW (2017) Real-time DNA sequencing in the Antarctic dry valleys using the Oxford Nanopore sequencer. J Biomol Tech 28(1):2–7

    Article  PubMed  PubMed Central  Google Scholar 

  • Jones JB, Sasser WE Jr (2001) Laboratory guide for conducting soil tests and plant analysis. CRC, Boca Raton, London, New York, Washington, DC

    Book  Google Scholar 

  • Kimathi RH, Wilisiani F, Mashiko T, Neriya Y, Miinda AE, Nishigawa H, Natsuaki T (2020) First report of tomato chlorosis virus infecting tomato in Kenya. Sci Afr 7:e00286

    Google Scholar 

  • Koolivand D, Sokhandan-Bashir N, Behjatnia SAA, Jafari Joozani RA (2014) Detection of grapevine fanleaf virus by immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) with recombinant antibody. Arch Phytopathol Plant Prot 47(17):2070–2077

    Article  CAS  Google Scholar 

  • Kothari JD (2018) Plant disease identification using artificial intelligence: machine learning approach. Int J Innov Res Comput Commun Eng 7(11):11082–11085

    Google Scholar 

  • Leiva AM, Siriwan W, Lopez-Alvarez D, Barrantes I, Hemniam N, Saokham K, Cuellar WJ (2020) Nanopore-based complete genome sequence of a Sri Lankan cassava mosaic virus (Geminivirus) strain from Thailand. Microbiol Resour Announc 9(6):e01274–e01219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, He Z, Zhou J (2005) Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res 33(19):6114–6123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G (2008) A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. J Virol Methods 154(1–2):48–55

    Article  CAS  PubMed  Google Scholar 

  • Lichtenberg E, Olson LJ (2018) The fruit and vegetable import pathway for potential invasive pest arrivals. PLoS One 13(2):e0192280

    Article  PubMed  PubMed Central  Google Scholar 

  • Ling KS (2007) Molecular characterization of two Pepino mosaic virus variants from imported tomato seed reveals high levels of sequence identity between Chilean and US isolates. Virus Genes 34(1):1–8

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Wu K, Wu W, Mi W, Hao X, Wu Y (2019) A multiplex reverse transcription PCR assay for simultaneous detection of six main RNA viruses in tomato plants. J Virol Methods 265:53–58

    Article  CAS  PubMed  Google Scholar 

  • Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M (2012) Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family Geminiviridae. Virology 432(1):162–172

    Article  CAS  PubMed  Google Scholar 

  • Lodha TD, Basak J (2012) Plant–pathogen interactions: what microarray tells about it? Mol Biotechnol 50(1):87–97

    Article  CAS  PubMed  Google Scholar 

  • Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68(10):5064–5081

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu H, Giordano F, Ning Z (2016) Oxford Nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinformatics 14(5):265–279

    Article  PubMed  PubMed Central  Google Scholar 

  • Lucas JA (1998) Plant pathology and plant pathogens. Blackwell Science, Oxford

    Google Scholar 

  • Maina S, Edwards OR, de Almeida L, Ximenes A, Jones RA (2017) Metagenomic analysis of cucumber RNA from East Timor reveals an aphid lethal paralysis virus genome. Genome Announc 5(2):e01445–e01416

    Article  PubMed  PubMed Central  Google Scholar 

  • Maree HJ, Fox A, Al Rwahnih M, Boonham N, Candresse T (2018) Application of HTS for routine plant virus diagnostics: state of the art and challenges. Front Plant Sci 9:1082

    Article  PubMed  PubMed Central  Google Scholar 

  • Mehetre GT, Paranjpe AS, Dastager SG, Dharne MS (2018) Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India. Genomics Data 7:140–143

    Article  Google Scholar 

  • Mehetre GT, Leo VV, Singh G, Sorokan A, Maksimov I, Yadav MK, Upadhyaya K, Hashem A, Alsaleh AN, Dawoud TM, Almaary KS (2021) Current developments and challenges in plant viral diagnostics: a systematic review. Viruses 13(3):412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Monger WA, Goodfellow HA, Back EJ (2020) First report of Arabis mosaic virus in potato (Solanum tuberosum), identified by nanopore sequencing. N Dis Rep 41:29

    Article  Google Scholar 

  • Mumo NN, Mamati GE, Ateka EM, Rimberia FK, Asudi GO, Boykin LM, Machuka EM, Njuguna JN, Pelle R, Stomeo F (2020) Metagenomic analysis of plant viruses associated with papaya ringspot disease in Carica papaya L. in Kenya. Front Microbiol 11:205

    Article  PubMed  PubMed Central  Google Scholar 

  • Mur LA, Kenton P, Lloyd AJ, Ougham H, Prats E (2008) The hypersensitive response; the centenary is upon us but how much do we know? J Exp Bot 59(3):501–520

    Article  CAS  PubMed  Google Scholar 

  • Murali A, Bhargava A, Wright ES (2018) IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome 6(1):1–14

    Article  Google Scholar 

  • Nateqi M, Habibi MK, Dizadji A, Parizad S (2015) Detection and molecular characterization of the iris severe mosaic virus-Ir isolate from Iran. J Plant Prot Res 55(3):235–240

    Article  CAS  Google Scholar 

  • Newton AC, Fitt BDL, Atkins SD, Walters DR, Daniell TJ (2010) Pathogenesis, parasitism and mutualism in the trophic space of microbe-plant interactions. Trends Microbiol 18:365–373

    Article  CAS  PubMed  Google Scholar 

  • Nguyen M, Wemheuer B, Laffy PW, Webster NS, Thomas T (2021) Taxonomic, functional and expression analysis of viral communities associated with marine sponges. PeerJ 12(2):2–21

    Google Scholar 

  • Nhlapo TF, Rees DJG, Odeny DA, Mulabisana JM, Rey MEC (2018) Viral metagenomics reveals sweet potato virus diversity in the eastern and Western cape provinces of South Africa. South Afr J Bot 117:256–267

    Article  Google Scholar 

  • Pal T, Jaiswal V, Chauhan RS (2016) DRPPP: a machine learning based tool for prediction of disease resistance protein in plants. Comput Biol Med 78:42–48

    Article  CAS  PubMed  Google Scholar 

  • Payne A, Holmes N, Rakyan V, Loose M (2019) BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files. Bioinformatics 35(13):2193–2198

    Article  CAS  PubMed  Google Scholar 

  • Pena JM, Torres-Sanchez J, Serrano-Perez A, de Castro AI, Lopez-Granados F (2015) Quantifying efficacy and limits of unmanned aerial vehicle (UAV) technology for weed seedling detection as affected by sensor resolution. Sensors 15:5609–5626

    Article  PubMed  PubMed Central  Google Scholar 

  • Peplies J, Glöckner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69(3):1397–1407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pothuganti K (2013) An efficient architecture for lifting based 3D-discrete wavelet transform. Int J Eng Res Technol 2(12):2278–2018

    Google Scholar 

  • Quince C, Walker AW, Simpson JT, Loman NJ, Segata N (2017) Correction: corrigendum: shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35(12):1211–1211

    Article  CAS  PubMed  Google Scholar 

  • Ratushna VG, Weller JW, Gibas CJ (2005) Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics 6(1):1–13

    Article  Google Scholar 

  • Rizzo DM, Garbelotto M, Davidson JM, Slaughter GW, Koike ST (2002) Phytophthora ramorum as the cause of extensive mortality of Quercus spp. and Lithocarpus densiflorus in California. Plant Dis 86(3):205–214

    Article  CAS  PubMed  Google Scholar 

  • Saunders DG, Win J, Cano LM, Szabo LJ, Kamoun S, Raffaele S (2012) Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi. PLoS One 7:e29847

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Segarra G, Casanova E, Bellido D, Odena MA, Oliveira E, Trillas I (2007) Proteome, salicylic acid, and jasmonic acid changes in cucumber plants inoculated with Trichoderma asperellum strain T34. Proteomics 7(21):3943–3952

    Article  CAS  PubMed  Google Scholar 

  • Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9(8):811–814

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sinha S, Samad A (2019) First report of cucumber mosaic virus associated with yellowing mosaic disease of African basil (Ocimum gratissimum) in India. Plant Dis 103(1):167

    Article  Google Scholar 

  • Snijesh VP, Singh S (2014) Molecular modeling and network based approach in explaining the medicinal properties of Nyctanthes arbortristis, Lippia nodiflora for rheumatoid arthritis. J Bioinform Intell Cont 3(1):31–38

    Article  Google Scholar 

  • Solden L, Lloyd K, Wrighton K (2016) The bright side of microbial dark matter: lessons learned from the uncultivated majority. Curr Opin Microbiol 31:217–226

    Article  PubMed  Google Scholar 

  • Soni AN (2018) Feature extraction methods for time series functions using machine learning. Int J Innov Res Sci Eng Technol 7(8):8661–8665

    Google Scholar 

  • Staal YC, van Herwijnen MH, van Schooten FJ, van Delft JH (2005) Application of four dyes in gene expression analyses by microarrays. BMC Genomics 6(1):1–13

    Article  Google Scholar 

  • Steinberg KM, Schneider VA, Alkan C, Montague MJ, Warren WC, Church DM, Wilson RK (2017) Building and improving reference genome assemblies. Proc IEEE 105(3):422–435

    CAS  Google Scholar 

  • Stobbe AH, Roossinck MJ (2014) Plant virus metagenomics: what we know and why we need to know more. Front Plant Sci 5:150

    Article  PubMed  PubMed Central  Google Scholar 

  • Theuns S, Vanmechelen B, Bernaert Q, Deboutte W, Vandenhole M, Beller L, Matthijnssens J, Maes P, Nauwynck HJ (2018) Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus. Sci Rep 8(1):1–13

    Article  CAS  Google Scholar 

  • Úrbez-Torres JR, Haag P, Bowen P, Lowery T, O’Gorman DT (2015) Development of a DNA macroarray for the detection and identification of fungal pathogens causing decline of young grapevines. Phytopathology 105(10):1373–1388

    Article  PubMed  Google Scholar 

  • Valcu CM, Junqueira M, Shevchenko A, Schlink K (2009) Comparative proteomic analysis of responses to pathogen infection and wounding in Fagus sylvatica. J Proteome Res 8(8):4077–4091

    Article  CAS  PubMed  Google Scholar 

  • van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C (2018) The third revolution in sequencing technology. Trends Genet 34(9):666–681

    Article  PubMed  Google Scholar 

  • Verma N, Sao P, Srivastava A, Singh S (2021) Physiological and molecular responses to drought, submergence and excessive watering in plants. In: Harsh environment and plant resilience: molecular and functional aspects, pp 305–321

    Chapter  Google Scholar 

  • Vigne E, Garcia S, Komar V, Lemaire O, Hily JM (2018) Comparison of serological and molecular methods with high-throughput sequencing for the detection and quantification of grapevine fanleaf virus in vineyard samples. Front Microbiol 9:2726

    Article  PubMed  PubMed Central  Google Scholar 

  • Villamor DEV, Mekuria TA, Pillai SS, Eastwell KC (2016) High-throughput sequencing identifies novel viruses in nectarine: insights to the etiology of stem-pitting disease. Phytopathology 106(5):519–527

    Article  CAS  PubMed  Google Scholar 

  • Vinayarani G, Madhusudhan KN, Deepak SA, Niranjana SR, Prakash HS (2011) Detection of mixed infection of tobamoviruses in tomato and bell pepper by using RT-PCR and duplex RT-PCR. Int J Plant Pathol 2(2):89–95

    Article  Google Scholar 

  • Voinnet O (2001) RNA silencing as a plant immune system against viruses. Trends Genet 17(8):449–459

    Article  CAS  PubMed  Google Scholar 

  • Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840. https://doi.org/10.1038/nrmicro2910

    Article  CAS  PubMed  Google Scholar 

  • Wang W, Guo J, Wang Z, Wang H, Cheng J, Wang C, Yuan M, Kurths J, Luo X, Gao Y (2021) Abnormal flow detection in industrial control network based on deep reinforcement learning. Appl Math Comput 409:126379

    Google Scholar 

  • Xiang CC, Kozhich OA, Chen M, Inman JM, Phan QN, Chen Y, Brownstein MJ (2002) Amine-modified random primers to label probes for DNA microarrays. Nat Biotechnol 20(7):738–742

    Article  CAS  PubMed  Google Scholar 

  • Xu J (2016) Fungal DNA barcoding. Genome 59(11):913–932

    Article  CAS  PubMed  Google Scholar 

  • Xue L, Yamazaki H, Ren R, Wanunu M, Ivanov AP, Edel JB (2020) Solid-state nanopore sensors. Nat Rev Mater 5(12):931–951

    Article  CAS  Google Scholar 

  • Zhang C, Timmis R, Hu WS (1999) A neural network based pattern recognition system for somatic embryos of Douglas fir. Plant Cell Tiss Org Cult 56(1):25–35

    Article  Google Scholar 

  • Zhang N, McCarthy ML, Smart CD (2008) A macroarray system for the detection of fungal and oomycete pathogens of solanaceous crops. Plant Dis 92(6):953–960

    Article  CAS  PubMed  Google Scholar 

  • Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J (2020) Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 1099:1–15. https://doi.org/10.1016/j.aca.2019.11.056

    Article  CAS  PubMed  Google Scholar 

  • Zhao L, Yang W, Zhang Y, Wu Z, Wang QC, Wu Y (2019) Occurrence and molecular variability of kiwifruit viruses in Actinidia deliciosa ‘Xuxiang’ in the Shaanxi province of China. Plant Dis 103(6):1309–1318

    Article  CAS  PubMed  Google Scholar 

  • Zipfel C (2008) Pattern-recognition receptors in plant innate immunity. Curr Opin Immunol 20(1):10–16

    Article  CAS  PubMed  Google Scholar 

  • Zulak KG, Khan MF, Alcantara J, Schriemer DC, Facchini PJ (2009) Plant defense responses in opium poppy cell cultures revealed by liquid chromatography-tandem mass spectrometry proteomics. Mol Cell Proteomics 8(1):86–98

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Faculty of Biotechnology, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Lucknow, Uttar Pradesh, India

    Rahat Parveen & Noopur Khare

  2. Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India

    Sachidanand Singh

  3. Department of Biotechnology, Dr. Ambedkar Institute of Technology for Handicapped, Kanpur, Uttar Pradesh, India

    Parul Johri

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  1. ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, Uttar Pradesh, India

    Udai B. Singh

  2. Division of Crop Protection, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India

    Ravindra Kumar

  3. Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India

    Harikesh Bahadur Singh

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© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

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Parveen, R., Khare, N., Singh, S., Johri, P. (2023). An In Silico Outlook for the Detection and Surveillance of Evolving and Persistent Plant Pathogens. In: Singh, U.B., Kumar, R., Singh, H.B. (eds) Detection, Diagnosis and Management of Soil-borne Phytopathogens. Springer, Singapore. https://doi.org/10.1007/978-981-19-8307-8_2

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