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BioData Mining

, 7:25

First Online: 07 November 2014Received: 11 July 2014Accepted: 25 October 2014

Abstract

BackgroundMany bacterial genome sequences completed using the Sanger method may contain assembly errors due in-part to low sequence coverage driven by cost.

FindingsTo illustrate the need for re-sequencing of pre-nextgen genomes and to validate sequenced genomes, we conducted a series of experiments, using high coverage sequencing data generated by a Illumina Miseq sequencer to sequence genomic DNAs of Bacteroides fragilis NCTC 9343, Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150, Vibrio cholerae O1 biovar El Tor str. N16961, Bacillus halodurans C-125 and Caulobacter crescentus CB15, which had previously been sequenced by the Sanger method during the early 2000’s.

ConclusionsThis study revealed a number of discrepancies between the published assemblies and sequence read alignments for all five bacterial species, suggesting that the continued use of these error-containing genomes and their genetic information may contribute to false conclusions and-or incorrect future discoveries when they are used.

KeywordsMicrobiota Genomics Genomes Bacteria Sequences Salmonella Mycobacterium Brucella Vibrio Electronic supplementary materialThe online version of this article doi:10.1186-1756-0381-7-25 contains supplementary material, which is available to authorized users.

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Author: Hongseok Tae - Enusha Karunasena - Jasmin H Bavarva - Harold R Garner

Source: https://link.springer.com/



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