Updating microbial genomic sequences: Improving accuracy & innovation

Hongseok Tae, Enusha Karunasena, Jasmin H. Bavarva, Harold R. Garner

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number122
JournalBioData Mining
Volume7
Issue number1
DOIs
StatePublished - Nov 7 2014

Keywords

  • Bacteria
  • Brucella
  • Genomes
  • Genomics
  • Microbiota
  • Mycobacterium
  • Salmonella
  • Sequences
  • Vibrio

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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