Obtaining a Fast and Reliable Diagnostic Result of Acidovorax Citrulli with the Sample Enrichment Method

Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.

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Selective pre-enrichment method to lessen time needed to recover Salmonella from commercial poultry processing samples

Food Microbiology ◽

10.1016/j.fm.2021.103818 ◽

2021 ◽

Vol 99 ◽

pp. 103818

Author(s):

Surendra Rasamsetti ◽

Mark Berrang ◽

Nelson A. Cox ◽

Nikki W. Shariat

Keyword(s):

Enrichment Method ◽

Poultry Processing ◽

Commercial Poultry

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Development of Molecular Markers for Detection of Acidovorax citrulli Strains Causing Bacterial Fruit Blotch Disease in Melon

International Journal of Molecular Sciences ◽

10.3390/ijms20112715 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2715 ◽

Cited By ~ 1

Author(s):

Md. Rafiqul Islam ◽

Mohammad Rashed Hossain ◽

Hoy-Taek Kim ◽

Denison Michael Immanuel Jesse ◽

Md. Abuyusuf ◽

...

Keyword(s):

Infected Leaf ◽

Bacterial Fruit Blotch ◽

Early Disease Detection ◽

Acidovorax Citrulli ◽

Seed Health ◽

Field Samples ◽

Whole Genomes ◽

Pathogenesis Related ◽

Primer Sets ◽

Inoculation Assay

Acidovorax citrulli (A. citrulli) strains cause bacterial fruit blotch (BFB) in cucurbit crops and affect melon significantly. Numerous strains of the bacterium have been isolated from melon hosts globally. Strains that are aggressively virulent towards melon and diagnostic markers for detecting such strains are yet to be identified. Using a cross-inoculation assay, we demonstrated that two Korean strains of A. citrulli, NIHHS15-280 and KACC18782, are highly virulent towards melon but avirulent/mildly virulent to the other cucurbit crops. The whole genomes of three A. citrulli strains isolated from melon and three from watermelon were aligned, allowing the design of three primer sets (AcM13, AcM380, and AcM797) that are specific to melon host strains, from three pathogenesis-related genes. These primers successfully detected the target strain NIHHS15-280 in polymerase chain reaction (PCR) assays from a very low concentration of bacterial gDNA. They were also effective in detecting the target strains from artificially infected leaf, fruit, and seed washing suspensions, without requiring the extraction of bacterial DNA. This is the first report of PCR-based markers that offer reliable, sensitive, and rapid detection of strains of A. citrulli causing BFB in melon. These markers may also be useful in early disease detection in the field samples, in seed health tests, and for international quarantine purposes.

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Tn5 transposon mutagenesis in Acidovorax citrulli for identification of genes required for pathogenicity on cucumber

Plant Pathology ◽

10.1111/j.1365-3059.2011.02519.x ◽

2011 ◽

Vol 61 (2) ◽

pp. 364-374 ◽

Cited By ~ 2

Author(s):

J. Liu ◽

S. Z. Luo ◽

Q. Zhang ◽

Q. H. Wang ◽

J. F. Chen ◽

...

Keyword(s):

Transposon Mutagenesis ◽

Tn5 Transposon ◽

Acidovorax Citrulli

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Detection of Vibrio cholerae and Vibrio parahaemolyticus by molecular and culture based methods from source water to household container-stored water at the point-of-use in South African rural communities

Water Science & Technology ◽

10.2166/wst.2010.222 ◽

2010 ◽

Vol 61 (12) ◽

pp. 3091-3101 ◽

Cited By ~ 7

Author(s):

V. M. Ntema ◽

N. Potgieter ◽

T. G. Barnard

Keyword(s):

16S Rrna ◽

Vibrio Cholerae ◽

Vibrio Parahaemolyticus ◽

Pcr Detection ◽

Toxin Gene ◽

Specific Method ◽

Culturable Bacteria ◽

Source Water ◽

Enrichment Method ◽

Filtration Enrichment

Detection methods for Vibrio cholerae and Vibrio parahaemolyticus which included the culture based approach with polymerase chain reaction (PCR) confirmation, PCR detection without enrichment and PCR with a pre-enrichment were developed and their performance evaluated. PCR assays targeted the SodB (V. cholerae species), Flae (V. parahaemolyticus species), 16S rRNA (Vibrio and Enterobacteriacea species) genes (Multiplex 1) and V. cholerae O1 and V. cholerae O139 rfb genes, ctxA (cholera toxin) gene and 16S rRNA gene (Multiplex 2). These methods were used to determine the occurrence of selected Vibrios in source water as well as in household container-stored water. The combination of filtration, enrichment and PCR method provided a sensitive and specific method for the detection of selected Vibrios in water samples. The PCR with a pre-enrichment method detected as few as 4–10 cfu/100 mL of selected Vibrios and PCR detection without the enrichment method detected as few as 40–100 cfu/100 mL of selected Vibrios. The inclusion of an enrichment period allows detection of culturable bacteria. As an application of the developed methods, V. cholerae and V. parahaemolyticus were detected in the source water used by the population and in the water-storage containers. The results indicate that Vibrio species in the containers could have originated from the source water and survive in biofilms inside the containers.

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