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The intensities of most of the AFLP markers for strain CB CBB markers) were already very faint in the unselected (control) cross progeny compared to the intensity of the corresponding AFLP bands in the parental strain CB.
Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.
Following AJ-specific immune selection, 24 of the 197 AFLP markers for strain AJ (AJ markers) (12.2% of AJ specific markers) had CIs of less than 50% under AJ-specific immune selection (i.e. intensity reduction of greater than 50% relative to growth of the cross progeny in the non-immune batch mate), listed in Table 2.
Since BIMEs exhibit exceptional length polymorphism, they have been utilized as reliable markers for strain determination.
The minicircle variable regions that encode the gRNAs have been used as molecular markers for strain genotyping and comparison [ 14].
In recent emergent pathogens, TRs are a source of very informative markers for strain genotyping [ 12, 13].
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Use of molecular markers for strain-specific differentiation of Mycobacterium tuberculosis-complex (MTBC) isolates in epidemiological studies became available in the last decades.
With sequencing becoming ever more affordable and accurate [ 31] we will be able to sequence the mitochondrial maxicircle from representatives of each DTU and re-evaluate the three-clade scheme to redefine or further confirm the population structure as well as uncover markers for strains and clades to better understand Chagas disease.
Notably, the A. marginale surface protein 1a (MSP1a) is a model molecule for these studies because it serves as a marker for strain identity, is both an adhesin necessary for infection of cells and an immuno-reactive protein and is also an indicator of the evolution of strain diversity.
IS6110 is a powerful genetic marker for strain differentiation [ 12].
Our findings confirm observations that hemolysis is not a reliable marker for strain discrimination.
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