Australasian Plant Pathology最新文献

{"title":"Characterization and functional validation of a genomic region involved in resistance to rust race II in Coffea arabica","authors":"Caroline Ariyoshi,&nbsp;Suzana Tiemi Ivamoto-Suzuki,&nbsp;Viviane Yumi Baba,&nbsp;Masako Toma-Braghini,&nbsp;Gustavo Hiroshi Sera,&nbsp;Adrian Powell,&nbsp;Sandra Maria Bellodi Cação,&nbsp;Eveline Teixeira Caixeta,&nbsp;Luiz Filipe Protasio Pereira","doi":"10.1007/s13313-024-00988-2","DOIUrl":"10.1007/s13313-024-00988-2","url":null,"abstract":"<div><p>Coffee leaf rust (CLR) is one of the most economically important diseases affecting <i>Coffea arabica</i> production, having a significant economic impact. Among the main goals of coffee breeding programs is the development of cultivars resistant to this disease. A source of resistance genes is Híbrido de Timor (HdT), a spontaneous hybrid originated from the cross between <i>C. arabica</i> and <i>C. canephora</i>. Previously, in a transcriptome study, the <i>Ca TDF77 NBS-LRR</i> gene from HdT involved in resistance to CLR was identified. Hence, our aim was to characterize the genomic region surrounding the <i>Ca TDF77 NBS-LRR</i> gene in <i>Coffea</i> spp. Furthermore, we aimed to analyze the transcriptional profile of this gene, in the <i>C. arabica</i> cultivar IAPAR 59, which is originated from HdT introgression and is resistant to CLR race II. The outcome delineated the gene’s localization on chromosome 11 (canephora subgenome) of <i>C. arabica</i>, spotlighting intragenic polymorphisms between HdT and Arabica coffee susceptible to CLR race II. The genomic region surrounding the gene in <i>Coffea</i> spp. revealed a tandem structure and transposable elements. Notably, within IAPAR 59, the gene exhibited significant upregulation at 24 and 72 h post CLR infection, contrasting starkly with the susceptible genotype. This observation validates its role in fortifying the defense mechanism of this particular cultivar. This study enriches our understanding of the evolutionary dynamics of <i>Coffea</i> spp. genomes and also provides genomic resources instrumental in devising biotechnological strategies for resistance to CLR.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"363 - 373"},"PeriodicalIF":0.9,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the role of nitrogen and silicon regimes in rice blast management and yield performance of Mushk Budji variety under field conditions","authors":"Zakir Amin,&nbsp;F. A. Mohiddin,&nbsp;Ali Anwar,&nbsp;Asif. B. Shikari,&nbsp;Tauseef A. Bhat,&nbsp;Fehim Jeelani Wani,&nbsp;T. A. Raja,&nbsp;Zahoor Ahmad Baba,&nbsp;Najeebul Rehman Sofi,&nbsp;Shugufta Parveen,&nbsp;Heena Altaf","doi":"10.1007/s13313-024-00986-4","DOIUrl":"10.1007/s13313-024-00986-4","url":null,"abstract":"<div><p>This study investigated the interactive effects of nitrogen and silicon fertilization on disease incidence, severity, grain yield, and straw yield in susceptible rice variety under rice blast disease pressure across two consecutive years. The results revealed significant variations in disease parameters across different nutrient combinations. The study involved four levels each of nitrogen (N₀: 0 Kg/ha; N₁:50 Kg/ha; N₂: 100 Kg/ha and N₃: 150 Kg/ha) and silicon (Si₀: 0 Kg/ha; Si₁: 60 Kg/ha; Si₃: 90 Kg/ha and Si₃: 120 Kg/ha). The treatments with lower to moderate nitrogen levels coupled with higher silicon rates exhibited the lowest disease incidence and severity, highlighting their synergistic effect in enhancing disease resistance. Conversely, high nitrogen levels with low or no silicon supplementation displayed the highest disease susceptibility, indicating that excessive nitrogen without adequate silicon can exacerbate vulnerability. Notably, increasing silicon levels led to decreasing disease incidence and severity, while the opposite trend was observed for nitrogen, underscoring silicon’s pivotal role in mitigating disease impact. Regarding yield parameters, the highest silicon rate (120 kg/ha) consistently resulted in superior grain yields, particularly when combined with moderate nitrogen levels (100 Kg/ha). The positive effect of silicon on grain yield was more pronounced at lower nitrogen levels, suggesting its potential to compensate for nitrogen deficiency. Moreover, the highest silicon level consistently exhibited superior straw yields across nitrogen levels. However, moderate nutrient levels occasionally outperformed the highest levels, implying an optimum range for maximizing straw yield while avoiding yield penalties associated with excessive application.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"353 - 362"},"PeriodicalIF":0.9,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response to the detection of Fusarium dieback associated with ambrosia beetles on Acer negundo in New South Wales","authors":"Sophia Callaghan,&nbsp;Angus J. Carnegie,&nbsp;Peter Gillespie,&nbsp;Shannon Mulholland,&nbsp;Matthew Nagel,&nbsp;David Sargeant,&nbsp;Andrew Daly,&nbsp;Ossie Wildman","doi":"10.1007/s13313-024-00984-6","DOIUrl":"10.1007/s13313-024-00984-6","url":null,"abstract":"<div><p>Symptoms consistent with polyphagous shot hole borer (<i>Euwallacea fornicatus</i>) and <i>Fusarium</i> dieback (<i>Fusarium euwallaceae</i>), recognised as high priority environmental pests for Australia, were observed on a single box elder (<i>Acer negundo)</i> tree in Sydney, New South Wales, in March 2022 during routine forest biosecurity surveillance. Delimiting surveys were undertaken around the Sydney basin, extending radially from the original box elder, resulting in the detection of a further three box elder and one tuckeroo (<i>Cupaniopsis anacardioides</i>) with suspicious symptoms. Samples were taken from the five trees and associated beetles diagnosed using morphological and molecular methods. Associated <i>Fusarium</i>-like fungi were identified according to phylogenetic inference using regions of the internal transcribed spacer, as well as the translation elongation factor 1-α and RNA polymerase II genes. The tea shot hole borer, <i>Euwallacea perbrevis</i>, was identified along with its known fungal mutualist, <i>Fusarium obliquiseptatum</i>. This pair have been reported in Queensland on avocado (<i>Persea americana</i>) and tuckeroo, and there are unpublished records of <i>E. perbrevis</i> from northern NSW, but this is the first report of both species occurring simultaneously in NSW. The biosecurity response following the initial detection, including the establishment of an Incident Management Team, surveillance, diagnostics, and stakeholder engagement, is discussed. This paper highlights the importance of surveillance for early detection of invasive pests and biosecurity systems and processes for enabling a timely response.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"345 - 352"},"PeriodicalIF":0.9,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s13313-024-00984-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of plasmid and its role in phytopathogenic bacteria Xanthomonas citri pv. viticola strains","authors":"Sneha Bhosale,&nbsp;Sujoy Saha,&nbsp;Nayana Patil","doi":"10.1007/s13313-024-00982-8","DOIUrl":"10.1007/s13313-024-00982-8","url":null,"abstract":"<div><p>The most significant bacterial disease infecting grape is bacterial leaf spot (BLS), caused by <i>Xanthomonas citri</i> pv. <i>viticola</i> (<i>Xcv</i>) strain. In the field, BLS severity depends on host genotype, pathogen pressure and environmental conditions. Plasmids, the extra chromosomal DNA components of phytopathogenic bacteria, play a crucial role in disease development as well as in the diverse evolution of the pathogen. Genome diversity and distribution of genes responsible for various factors present on plasmid in the pathogen are not well understood. The current research aimed to investigate various plasmid-borne traits in <i>Xcv</i> strains collected from twenty-three different locations. Four different curing agents viz. ethidium bromide (EtBr), acridine orange (AO), sodium dodecyl sulphate (SDS) and elevated heat were used to cure the plasmid. The findings revealed uniform plasmid size of approximately 23 kb among all isolates of India. The study also reveals the effect of plasmid curing on various traits, including morphology, pathogenicity, exopolysaccharide production, and antibiotic sensitivity. Exopolysaccharide production and pathogenicity were significantly reduced in the cured isolates. Cured <i>Xcv</i> isolates also exhibited significant variation in tested traits, displaying phenotypic differences in color, size, shape, elevation, appearance and margin. The study further emphasized the crucial role of plasmids as carriers for genetic exchange among plant pathogenic bacteria, contributing to bacterial adaptation to the environment. Additionally, the research highlighted the presence of antibiotic resistance traits on the plasmids and the importance of plasmid-mediated mechanisms in bacterial adaptation.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"325 - 334"},"PeriodicalIF":0.9,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of sources of resistance and comparative metabolomic profiling of resistant and susceptible chilli germplasm to Meloidogyne incognita Race 1","authors":"Prasanna Holajjer,&nbsp;T. P. Ahammed Shabeer,&nbsp;M. K. Mahatma,&nbsp;Z. Khan,&nbsp;S. R. Pandravada,&nbsp;N. Sivaraj,&nbsp;Anitha Kodaru,&nbsp;Anita Pardeshi","doi":"10.1007/s13313-024-00981-9","DOIUrl":"10.1007/s13313-024-00981-9","url":null,"abstract":"<div><p>Root-knot nematode, <i>Meloidogyne incognita</i> Kofoid and White, 1919 is a major endoparasite that causes significant economic losses in several Solanaceous crops worldwide, including chilli (<i>Capsicum annuum</i>). In the present study, 66 accessions were screened for sources of resistance to <i>M. incognita</i> Race 1. The accessions EC399535 and EC402105 showed less than 10 number of galls and egg mass per root system [RKI:2 (1–10 galls or egg mass/ root system)] and identified as resistant accessions against <i>M. incognita</i>. Further, metabolic profiling analysis in the roots of resistant and susceptible (EC378632 and Arka Lohit) accessions exposed to <i>M. incognita</i> was carried out using gas chromatography-mass spectrometry (GC-MS). Non-targeted metabolic analysis detected 116 metabolites, which were further subjected to partial least squares-discriminant analysis (PLS-DA) with variable importance in projection (VIP) score to measure accumulation pattern in resistant and susceptible genotypes. VIP score revealed that 14 metabolites showed higher accumulation (&gt; 1.5 VIP score) in resistant germplasm compared to susceptible germplasm. Specific metabolites viz., phytosterols, delta-tocopherol and squalene showed &gt; 2.0 VIP score. Heatmap analysis differentiated metabolite abundance in each germplasm under <i>M. incognita</i>-infected and non-infected conditions. Dendrogram clustering analysis of metabolites data clearly separated resistant and susceptible accessions. The most significant metabolic pathways activated in <i>M. incognita</i>-resistance were phenylalanine metabolism (0.23529 impact), and sesquiterpenoid and triterpenoid biosynthesis (0.21622 impact) and alanine, aspartate and glutamate metabolism (0.19784 impact). This study provides valuable insights into compounds involved in defense activities against <i>M. incognita</i>. However, more research on the nematostatic or nematicidal activities of these metabolites including chemical inhibition or gene silencing of metabolites in plants is required for understanding the resistance mechanism and utilizing these metabolites as a biomarkers in resistance breeding programme.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"313 - 324"},"PeriodicalIF":0.9,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling defense strategies: gene expression dynamics in blast-resistant vs. susceptible aromatic rice landraces","authors":"U. Keerthana,&nbsp;A. K. Senapati,&nbsp;Manas K. Bag,&nbsp;S. R. Prabhukarthikeyan,&nbsp;Shraddha B. Sawant,&nbsp;M. K. Mishra,&nbsp;S. D. Mohapatra","doi":"10.1007/s13313-024-00983-7","DOIUrl":"10.1007/s13313-024-00983-7","url":null,"abstract":"<div><p>In this study, efforts were made to understand the defence responses in resistant and susceptible aromatic landraces against the rice leaf blast pathogen, <i>Magnaporthe oryzae</i>. Four resistant genotypes (Benugopal, Manas, Karpurkali, and Kalazeera) and two susceptible genotypes (Kalikati 2 and Kalikati 1) underwent biochemical analysis in relation to blast disease. The results of the biochemical analysis revealed increased enzyme activity levels, namely peroxidase, phenylalanine ammonia-lyase, polyphenol oxidase, superoxide dismutase, and catalase, in the resistant genotypes (Benugopal (AC44184) and Karpurkali (AC44155)) in comparison to the susceptible ones [Kalikati 2 (AC44236) and Kalikati 1 (AC44156)]. The same trend has been seen in the assays for β-1,3-glucanase and total phenols. RT-qPCR evaluation has been performed to establish the expression levels of PO, PAL, PPO, SOD, and CAT in the four resistant genotypes and the two susceptible ones after inoculation with <i>M. oryzae</i> (RLB 06) at various time intervals. Noteworthy variations in defence gene expression were noted among the genotypes. The expression of defence genes was upregulated in the resistant genotypes [Benugopal (AC44184) and Karpurkali (AC44155)] compared to their susceptible ones. Gene expression studies result indicated that the relative defence genes expression levels related to the spectrophotometric data.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"335 - 343"},"PeriodicalIF":0.9,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kale (Brassica oleracea L. var. acephala) rhizosphere bacteria suppress Pythium aphanidermatum-induced damping-off of cabbage, produce biofilm and antimicrobial volatile compounds","authors":"Al-Galya Essa Al-Rubkhi,&nbsp;Abdullah Mohammed Al-Sadi,&nbsp;Rhonda Janke,&nbsp;Issa Hashil Al-Mahmooli,&nbsp;Majida Mohammed Ali Al-Harrasi,&nbsp;Rethinasamy Velazhahan","doi":"10.1007/s13313-024-00980-w","DOIUrl":"10.1007/s13313-024-00980-w","url":null,"abstract":"<div><p>In this study, rhizosphere and endophytic bacteria of kale (<i>Brassica oleracea</i> L. var. <i>acephala</i>) cultivars ‘Winterbor’ and ‘Black Magic’ were isolated and their efficacy to suppress damping-off of cabbage caused by <i>Pythium aphanidermatum</i> was evaluated. On nutrient agar medium, 10 bacterial isolates with different morphological characteristics were isolated from kale roots and rhizosphere soil. In an in vitro dual culture assay, two rhizosphere bacterial isolates (KRB1 and KRB2) obtained from ‘Winterbor’ exhibited high levels of inhibitory activity against the mycelial growth of <i>P. aphanidermatum</i>. Based on 16S rDNA sequence analysis, these bacterial isolates were identified as <i>Pseudomonas alcaligenes</i> (KRB1) and <i>Rheinheimera mangrovi</i> (KRB2). Soil application of <i>P. alcaligenes</i> KRB1 and <i>R. mangrovi</i> KRB2 reduced the damping-off incidence in cabbage by 42.4% and 45.5%, respectively compared to the infected control under controlled pot culture conditions. Both bacterial strains demonstrated the ability to form biofilm; however, <i>P. alcaligenes</i> KRB1 produced five times more biofilm than <i>R. mangrovi</i> KRB2. These bacterial strains produced volatile compounds that suppressed <i>P. aphanidermatum</i> growth in an in vitro assay. Gas chromatography-mass spectrometry analysis of volatile compounds revealed that <i>P. alcaligenes</i> KRB1 and <i>R. mangrovi</i> KRB2 predominantly produced L-alanine ethylamide, (S)-, accounting for 35.9% and 29.5% of the peak area, respectively. The capability to form biofilms and release anti-oomycete volatile compounds likely contributes to the biocontrol effectiveness of these bacterial strains against <i>P. aphanidermatum</i>.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"305 - 312"},"PeriodicalIF":0.9,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141354508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid detection of chilli leaf curl virus using loop-mediated isothermal amplification","authors":"J. M. Catherine,&nbsp;Masilamani Karthikeyan,&nbsp;Pasupathi Rathinasabapathi","doi":"10.1007/s13313-024-00979-3","DOIUrl":"10.1007/s13313-024-00979-3","url":null,"abstract":"<div><p>Chilli leaf curl virus (ChiLCV) is a significant begomovirus that infects chili plants. To detect ChiLCV infection, a loop-mediated isothermal amplification (LAMP) assay was designed to be easy, quick, and efficient. The assay uses a set of five specific primers that target the coat protein gene (av1) of the target virus to detect the presence of the virus. The LAMP reaction amplifies the target gene within 45 min at 63 °C, with an 8mM dNTP concentration. This method showed no cross-reactivity with other tested begomoviruses that confirmed selective ChiLCV amplification. The sensitivity test revealed that LAMP was more sensitive than PCR. The LAMP assay displayed a remarkable detection limit of 10 fg/μL, which is superior than the PCR sensitivity of 10 pg/μL. Field sample validation yielded concordant results with PCR. This study introduces a cost-effective, and highly sensitive method for ChiLCV detection. Validation of LAMP with symptomatic leaves samples produced consistent results with PCR, demonstrating that the LAMP method could detect all infected samples.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 4","pages":"297 - 304"},"PeriodicalIF":0.9,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141191642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Why a strategic shift in action is needed to recognise and empower Indigenous plant pathology knowledge and research","authors":"H. Ehau-Taumaunu,&nbsp;N. M. Williams,&nbsp;A. Marsh,&nbsp;N. W. Waipara,&nbsp;C. M. Higgins,&nbsp;A. D. W. Geering,&nbsp;C. H. Mesarich,&nbsp;L. A. Rigano,&nbsp;B. A. Summerell,&nbsp;G. I. Johnson,&nbsp;P. Williamson,&nbsp;R. M. MacDiarmid","doi":"10.1007/s13313-024-00977-5","DOIUrl":"10.1007/s13313-024-00977-5","url":null,"abstract":"<div><p>Plant pathology researchers play a pivotal role in thought leadership and its translation to action regarding the recognition and demonstration of the value of Indigenous knowledge and science. For many scientists, navigating the space of Indigenous rights and perspectives is challenging. In pursuit of a cultural shift in research and development within the field of plant pathology, the 2019–2021 Management Committee of the Australasian Plant Pathology Society (APPS) undertook a review and modernization of the Society’s Constitution. The aim was to ensure its alignment with principles that foster inclusivity of Indigenous peoples in the development and implementation of relevant research projects impacting their communities. Additionally, a dynamic repository of guidelines and resources was compiled. These resources are designed to assist plant pathologists, while respecting and not superseding the guidance provided by local Indigenous researchers, practitioners, and advisors. The collective efforts of plant pathologists hold immense potential in championing Indigenous Peoples and their rights, steering the field toward a more inclusive and equitable future. This paper builds upon the thesis presented in the APPS Presidential Address at the Biennial APPS Conference in 2021, held virtually in lutruwita (Tasmania) on the unceded lands of the Palawa people. It underscores the potential impact when plant pathologists unite in advocating for Indigenous Peoples and their rightful place within the field.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 3","pages":"211 - 219"},"PeriodicalIF":0.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s13313-024-00977-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of NGS DNA barcoding for biosecurity diagnostic applications: case study from banana freckle incursion in Australia","authors":"Kalpani Galaihalage,&nbsp;Shreya Patel,&nbsp;Sonu Yadav","doi":"10.1007/s13313-024-00978-4","DOIUrl":"10.1007/s13313-024-00978-4","url":null,"abstract":"<div><p>Molecular diagnostics in combination with morphological identification is the method of choice for several cryptic microbial plant pathogens. For some diagnostic applications, traditional sequencing techniques can be time consuming, making them ill-suited for biosecurity incursion responses, where accurate results are needed in real time. More rapid next generation sequencing tools must be tested and compared with traditional methods to assess their utility in biosecurity applications. Here utilizing 95 samples infected with fungal pathogen <i>Phyllosticta cavendishii</i>, from a recent incursion in Australia, we compare species identification success using Internal Transcribed Spacer (ITS) gene barcode on conventional Sanger and Oxford Nanopore MinION sequencing platforms. For Sanger sequencing, the average pairwise identity percentage score between generated consensus sequences and <i>P. cavendishii</i> sequence from holotype material on NCBI database was 99.9% ± SE 0.0 whereas for MinION sequencing the average pairwise identity percentage was 99.1% ± SE 0.1. Relatively larger consensus sequences (mean 486 bp ± SE 2.4) were generated by Sanger sequencing compared to MinION sequencing (mean 435 bp ± SE 4.6). Our results confirm that both sequencing methods can reliably identify <i>P. cavendishii</i>. MinION sequencing, provided quicker results compared to Sanger sequencing and demonstrated diagnostic competence, with the added advantage of being portable, for front-line “point of incursion” biosecurity applications.</p></div>","PeriodicalId":8598,"journal":{"name":"Australasian Plant Pathology","volume":"53 3","pages":"291 - 295"},"PeriodicalIF":0.9,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s13313-024-00978-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}