Schematic representation of a range of hypothetical tRNA site configurations present in the four complete genomes (MG1655, CFT073, EDL933 and Sf301) (–)

Abstract

<p><b>Copyright information:</b></p><p>Taken from "A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria"</p><p>Nucleic Acids Research 2006;34(1):e3-e3.</p><p>Published online 9 Jan 2006</p><p>PMCID:PMC1326021.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The conserved UF and DF regions flanking tRNA genes are shown as dark grey filled boxes. UF and DF boxes drawn below the line indicate inversions with respect to the reference template MG1655 ( and ). The UF and DF boxes shown in pale grey with a broken outline represent deletions with respect to MG1655 ( and ). Genomic islands, where present, are indicated as broken boxes to emphasize the relatively large size of these regions. Arrowheads shown below each sub-figure indicate the location and orientation of primers specific to the UF and DF regions. Hollow arrowheads indicate the absence of matching complementary sequence. The solid line between the arrowheads shown in () indicates a likely successful PCR amplification; while the dotted line in () indicates a successful e-PCR-based ‘amplification’ that would typically yield a product of size far in excess of that that could be generated through standard PCR. The numbers shown above each configuration after the colon symbol represent the number of examples observed in the four genomes tested based on the 87 MG1655 tRNA genes and the total complement of orthologues present in the other three genomes (). The numbers of examples observed in the five unpublished genomes ( EAEC O42, EPEC E2348/69, ETEC E24377A, HS and 53G), with respect to the subset of 20 tRNA genes only (Supplementary Table S3), are shown in parentheses. The symbols shown alongside the drawings are used in and Supplementary Table S4 to highlight tRNA loci affected by inversions and/or deletions. Examples of the various atypical configurations observed in the four genomes are shown to the right. The figure is not drawn to scale