scholarly journals Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola

Plant Disease ◽  
2010 ◽  
Vol 94 (3) ◽  
pp. 311-319 ◽  
Author(s):  
Jillian M. Lang ◽  
John P. Hamilton ◽  
Maria Genaleen Q. Diaz ◽  
Marie Anne Van Sluys ◽  
Ma. Ruby G. Burgos ◽  
...  
Keyword(s):  
Bacterial Blight ◽  
Plant Pathogens ◽  
Diagnostic Marker ◽  
Xanthomonas Oryzae ◽  
Bacterial Leaf Streak ◽  
Chain Reaction ◽  
Associated Bacteria ◽  
Rice Bacterial Blight ◽  
Polymerase Chain ◽  
Genome Comparisons

A computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to rapidly identify unique regions for development of highly specific diagnostic markers. A suite of diagnostic primers was selected to monitor diverse loci and to distinguish the rice bacterial blight and bacterial leaf streak pathogens, Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. A subset of these primers was combined into a multiplex polymerase chain reaction set that accurately distinguished the two rice pathogens in a survey of a geographically diverse collection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola, other xanthomonads, and several genera of plant-pathogenic and plant- or seed-associated bacteria. This computational approach for identification of unique loci through whole-genome comparisons is a powerful tool that can be applied to other plant pathogens to expedite development of diagnostic primers.

CHAPTER 60: Polymerase Chain Reaction for Detection of Systemic Plant Pathogens

2011 ◽  
pp. 341-359 ◽  
Author(s):  
A. Hadidi ◽  
A. Olmos ◽  
G. Pasquini ◽  
M. Barba ◽  
R. R. Martin ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Plant Pathogens ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Vaginal and Extra-Vaginal Bacterial Colonization and Risk for Incident Bacterial Vaginosis in a Population of Women Who Have Sex With Men

2020 ◽  
Author(s):  
David N Fredricks ◽  
Anna Plantinga ◽  
Sujatha Srinivasan ◽  
Antoinette Oot ◽  
Andrew Wiser ◽  
...  
Keyword(s):  
Bacterial Vaginosis ◽  
Vaginal Discharge ◽  
Bacterial Colonization ◽  
Quantitative Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Associated Bacteria ◽  
Vaginal Colonization ◽  
Polymerase Chain ◽  
Sex With Men

Abstract Background Bacterial vaginosis (BV) is a common cause of vaginal discharge and associated with vaginal acquisition of BV-associated bacteria (BVAB). Methods We used quantitative polymerase chain reaction assays to determine whether presence or concentrations of BVAB in the mouth, anus, vagina, or labia before BV predict risk of incident BV in 72 women who have sex with men. Results Baseline vaginal and extra-vaginal colonization with Gardnerella spp, Megasphaera spp, Sneathia spp, BVAB-2, Dialister sp type 2, and other BVAB was more common among subjects with incident BV. Conclusions Prior colonization with BVAB is a consistent risk for BV.

scholarly journals Molecular and Pathotypic Characterization of New Xanthomonas oryzae Strains from West Africa

2007 ◽  
Vol 20 (5) ◽  
pp. 534-546 ◽  
Author(s):  
Carolina Gonzalez ◽  
Boris Szurek ◽  
Charles Manceau ◽  
Thierry Mathieu ◽  
Yacouba Séré ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
West Africa ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Xanthomonas Oryzae ◽  
Polymorphism Analysis ◽  
Transcription Activator ◽  
Chain Reaction ◽  
Polymerase Chain

DNA polymorphism analysis and pathogenicity assays were used to characterize strains of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola collected from rice leaves in West Africa. Restriction fragment length polymorphism (RFLP), repetitive sequence-based polymerase chain reaction, fluorescent amplified fragment-length polymorphism (FAFLP) analyses were assessed for molecular characterization, while pathogenicity was tested by leaf clipping and leaf infiltration. Dendrograms were generated for the data sets obtained from RFLP analysis and repetitive polymerase chain reaction suggesting that the interrelationships between strains were dependent on the technique used. In all cases, data showed that African strains of X. oryzae pv. oryzae form a group genetically distant from Asian strains. FAFLP analyses separated the X. oryzae strains into three groups with significant bootstrap values. A specific and intriguing feature of African strains of X. oryzae pv. oryzae is a reduction in the number of insertion sequence elements and transcription activator-like (avrBs3/pthA) effector genes, based on the molecular markers employed in the study. In addition, pathogenicity assays conducted with African strains of X. oryzae pv. oryzae on a series of nearly isogenic lines (NILs) identified three new races. Finally, leaf infiltration assays revealed the capacity of African strains of X. oryzae pv. oryzae to induce a nonhost hypersensitive response in Nicotiana benthamiana, in contrast with Asian X. oryzae pv. oryzae and X. oryzae pv. oryzicola strains. Our results reveal substantial differences between genomic characteristics of Asian and African strains of X. oryzae pv. oryzae.

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