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Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.

Puiu D, Salzberg SL - PLoS ONE (2008)

Bottom Line: F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness.We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly.This assembly will provide a more accurate basis for future comparative studies of this pathogen.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

ABSTRACT
Francisella tularensis is a highly infectious human intracellular pathogen that is the causative agent of tularemia. It occurs in several major subtypes, including the live vaccine strain holarctica (type B). F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness. Three complete genomes of subspecies holarctica have been sequenced and deposited in public archives, of which OSU18 was the first and the only strain for which a scientific publication has appeared. We re-assembled the OSU18 strain using both de novo and comparative assembly techniques, and found that the published sequence has two large inversion mis-assemblies. We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly. This assembly will provide a more accurate basis for future comparative studies of this pathogen.

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Related in: MedlinePlus

Hawkeye view of the AMOScmp assembly, showing pileup of mis-oriented reads (shown in red) in the chromosome region from position 167,086 to 184,936 (17,851 bp).See Figure 1 legend for detailed description.
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Related In: Results  -  Collection


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pone-0003427-g002: Hawkeye view of the AMOScmp assembly, showing pileup of mis-oriented reads (shown in red) in the chromosome region from position 167,086 to 184,936 (17,851 bp).See Figure 1 legend for detailed description.

Mentions: We inspected the suspected inversions in the AMOScmp reconstruction of CP000437 using the Hawkeye assembly viewer [14], which highlights regions that might be mis-assembled. As shown in Figures 1 and 2, the assembly based on CP000437 contains large pile-ups of mis-oriented reads (shown in red) flanking each inversion. Each red pair of reads in the figures represents two paired end sequences that are mis-oriented: in paired-end sequencing, both ends of a genomic fragment are sequenced, with the 5′ ends of the pair on the outer ends of the fragment. In the resulting assembly, the two sequences in a pair must be pointing “inward”; e.g., the positions of the reads must be in opposite orientations with the 5′ ends outermost and the 3′ ends innermost.


Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.

Puiu D, Salzberg SL - PLoS ONE (2008)

Hawkeye view of the AMOScmp assembly, showing pileup of mis-oriented reads (shown in red) in the chromosome region from position 167,086 to 184,936 (17,851 bp).See Figure 1 legend for detailed description.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2561293&req=5

pone-0003427-g002: Hawkeye view of the AMOScmp assembly, showing pileup of mis-oriented reads (shown in red) in the chromosome region from position 167,086 to 184,936 (17,851 bp).See Figure 1 legend for detailed description.
Mentions: We inspected the suspected inversions in the AMOScmp reconstruction of CP000437 using the Hawkeye assembly viewer [14], which highlights regions that might be mis-assembled. As shown in Figures 1 and 2, the assembly based on CP000437 contains large pile-ups of mis-oriented reads (shown in red) flanking each inversion. Each red pair of reads in the figures represents two paired end sequences that are mis-oriented: in paired-end sequencing, both ends of a genomic fragment are sequenced, with the 5′ ends of the pair on the outer ends of the fragment. In the resulting assembly, the two sequences in a pair must be pointing “inward”; e.g., the positions of the reads must be in opposite orientations with the 5′ ends outermost and the 3′ ends innermost.

Bottom Line: F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness.We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly.This assembly will provide a more accurate basis for future comparative studies of this pathogen.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

ABSTRACT
Francisella tularensis is a highly infectious human intracellular pathogen that is the causative agent of tularemia. It occurs in several major subtypes, including the live vaccine strain holarctica (type B). F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness. Three complete genomes of subspecies holarctica have been sequenced and deposited in public archives, of which OSU18 was the first and the only strain for which a scientific publication has appeared. We re-assembled the OSU18 strain using both de novo and comparative assembly techniques, and found that the published sequence has two large inversion mis-assemblies. We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly. This assembly will provide a more accurate basis for future comparative studies of this pathogen.

Show MeSH
Related in: MedlinePlus