Journal
BIODATA MINING
Volume 7, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/1756-0381-7-25
Keywords
Microbiota; Genomics; Genomes; Bacteria; Sequences; Salmonella; Mycobacterium; Brucella; Vibrio
Categories
Funding
- Medical Informatics and Systems Division
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Background: Many bacterial genome sequences completed using the Sanger method may contain assembly errors due in-part to low sequence coverage driven by cost. Findings: To 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. Conclusions: This 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.
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