Characterization and Comparison of Clavibacter michiganensis subsp. nebraskensis Strains Recovered from Epiphytic and Symptomatic Infections of Maize in Iowa

Abdolzadeh, Ahmad; Mbofung, Gladys Y.; Acharya, Jyotsna; Schmidt, Claude H.; Robertson, Alison E.

doi:10.1371/journal.pone.0143553

Cited by 24 publications

(14 citation statements)

References 25 publications

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“…V3 corn developmental stage plants were used for the inoculation following a slightly modified dropped‐wounded protocol described by Ahmad et al . (). The third leaf of each plant was wounded halfway between the sheath and the tip by making a cut across three veins on one side of the midrib.…”

Section: Methodsmentioning

confidence: 97%

Development of a loop‐mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis

2018

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Aims: Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis. Methods and Results: Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples. Conclusions:The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries. Significance and Impact of the Study: The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care.

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Section: Methodsmentioning

confidence: 97%

Development of a loop‐mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis

2018

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“…C. michiganensis ssp. nebraskensis strain 2581 isolated from maize does not carry any plasmids (Eichenlaub & Gartemann, 2011;Ahmad et al, 2015), and its putative virulence genes are located in the chromosome, although their identity and function have not been well studied (Tambong, 2017). C. michiganensis ssp.…”

Section: Introductionmentioning

confidence: 99%

Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper

Hwang

Kim

et al. 2017

New Phytologist

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Clavibacter michiganensis ssp. capsici is a Gram-positive plant-pathogenic bacterium causing bacterial canker disease in pepper. Virulence genes and mechanisms of C. michiganensis ssp. capsici in pepper have not yet been studied. To identify virulence genes of C. michiganensis ssp. capsici, comparative genome analyses with C. michiganensis ssp. capsici and its related C. michiganensis subspecies, and functional analysis of its putative virulence genes during infection were performed. The C. michiganensis ssp. capsici type strain PF008 carries one chromosome (3.056 Mb) and two plasmids (39 kb pCM1 and 145 kb pCM2 ). The genome analyses showed that this bacterium lacks a chromosomal pathogenicity island and celA gene that are important for disease development by C. michiganensis ssp. michiganensis in tomato, but carries most putative virulence genes in both plasmids. Virulence of pCM1 -cured C. michiganensis ssp. capsici was greatly reduced compared with the wild-type strain in pepper. The complementation analysis with pCM1 -located putative virulence genes showed that at least five genes, chpE, chpG, ppaA1, ppaB1 and pelA1, encoding serine proteases or pectate lyase contribute to disease development in pepper. In conclusion, C. michiganensis ssp. capsici has a unique genome structure, and its multiple plasmid-borne genes play critical roles in virulence in pepper, either separately or together.

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“…For single gene dnaA, the best evolution model was determined, and maximum likelihood (ML) method with 1,000 bootstrap values to evaluate node support was used to infer the phylogenetic tree. A color-coded matrix showing pairwise identity was generated using Sequence Demarcation Tool version 1.2 [23].…”

Section: Phylogenetic Analysismentioning

confidence: 99%

VIDHOP, viral host prediction with Deep Learning

Mock

Viehweger

Barth

et al. 2019

Preprint

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Zoonosis, the natural transmission of infections from animal to human, is a far-reaching global problem. The recent outbreaks of Zika virus and Ebola virus are examples of viral zoonosis, which occur more frequently due to globalization. In case of a virus outbreak, it is helpful to know which host organism was the original carrier of the virus. Once the reservoir or intermediate host is known, it can be isolated to prevent further spreading of the viral infection. Recent approaches aim to predict a viral host based on the viral genome, often in combination with the potential host genome and using arbitrary selected features. This methods have a clear limitation in either the amount of different hosts they can predict or the accuracy of the prediction. Here, we present a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. To assure a high prediction accuracy we developed an effective selection approach for the training data, to avoid biases due to a highly unbalanced number of known sequences per virus-host combinations. We tested our deep neural network on three different virus species (influenza A virus, rabies lyssavirus, rotavirus A) and reached for each virus species a AUC between 0.94 and 0.98, outperforming previous approaches and allowing highly accurate predictions while only using fractions of the viral genome sequences. We show that deep neural networks are suitable to predict the host of a virus, even with a limited amount of sequences and highly unbalanced available data. The deep neural networks trained for this approach build the core of the virus host predicting tool VIDHOP (VIrus Deep learning HOst Prediction). doi: bioRxiv preprint shown to perform well with character sequences 28 , such as DNA or RNA sequences, potentially allowing for a furthermore increase in the prediction quality. Author Contributions

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Characterization and Comparison of Clavibacter michiganensis subsp. nebraskensis Strains Recovered from Epiphytic and Symptomatic Infections of Maize in Iowa

Cited by 24 publications

References 25 publications

Development of a loop‐mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis

Development of a loop‐mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis

Multiple plasmid‐borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper

VIDHOP, viral host prediction with Deep Learning

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