Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

Tambong, James T.

doi:10.1371/journal.pone.0172295

Cited by 38 publications

(33 citation statements)

References 59 publications

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“…Genome analyses of C. michiganensis subspecies have been performed since the first report of the genome sequence of C. michiganensis ssp. michiganensis strain NCPPB382 (Bentley et al, 2008;Gartemann et al, 2008;Bae et al, 2015;Lu et al, 2015b;Tambong et al, 2015;Tambong, 2017). Genomic analysis of NCPPB382 revealed that it has a 130 kb chromosomal pathogenicity island (PAI) consisting of chp and tomA subregions, which include multiple virulence genes mostly encoding enzymes such as pectate lyase, serine proteases, and tomatinase, and this PAI region has been shown to play an important role in invasion of the host plant (Eichenlaub & Gartemann, 2011;Jackson et al, 2011).…”

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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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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“…Population genetic and comparative genomic analyses are imperative components for the development of robust and specific diagnostic tools (5,26,27,28). Multiple genome alignments using Mauve software resulted in highly conserved and unique gene regions specific for C. michiganensis in general (major facilitator superfamily gene) and specifically for C. m. subsp.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, primer set CM-dnaA-F/R, designed to amplify the dnaA partial-gene sequence of C. michiganensis, was used to confirm the identity of all nine subspecies (S1 Table). The housekeeping dnaA gene has been proven as a potential genetic marker for plant bacterial phylogenetic studies and identity confirmation [5].…”

Section: Discussionmentioning

confidence: 99%

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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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“…Michiganens infection. The genome of Cmm strain NCPPB382 ( Cmm382 ) identified the chp/tomA 129‐kb pathogenicity island that harbors serine proteases, cell wall degrading enzymes, and a tomatinase enzyme . Virulence factors involved in uptake and metabolism of carbohydrates and glycosyl hydrolases were in the tomA regions in the genome and in two plasmids (pCM1 and pCM2) .…”

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confidence: 99%

Refining a Pathogen's Genome to Know the Enemy Better for the Winning Battles

2019

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Clavibacter michiganensis, subsp. michiganens is a gram positive bacterial pathogen infecting tomato, resulting in the great losses of yield and quality worldwide. Despite its great impact on economics, we do not fully understand the virulence factors from its genome probably due to imperfect genome annotation. Peritore‐Galve et al. utilized proteogenomic approach to identify 26 novel protein‐coding regions, to extend 59 annotated open reading frames and to confirm protein expression for ≈70% of predicted gene models of Clavibacter michiganensis subsp. michiganensis. New findings by the proteogenomics technique were further confirmed using reverse transcription‐polymerase chain reaction. To win battles with pathogens, it is advantageous to know about our enemies accurately which can be achieved by mass spectrometry‐based identifications of novel protein‐coding regions in genomes.

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Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

Cited by 38 publications

References 59 publications

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

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

VIDHOP, viral host prediction with Deep Learning

Refining a Pathogen's Genome to Know the Enemy Better for the Winning Battles

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