Updating microbial genomic sequences: improving accuracy & innovation

BioData Mining

Hongseok Tae¹  Enusha Karunasena¹  Jasmin H Bavarva¹  Harold R Garner¹ 

[1] Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University, 1015 Life Sciences Circle, Blacksburg, VA 24061, USA

关键词: Vibrio;    Brucella;    Mycobacterium;    Salmonella;    Sequences;    Bacteria;    Genomes;    Genomics;    Microbiota;   

Others  :  1083989
DOI  :  10.1186/1756-0381-7-25

 received in 2014-07-11, accepted in 2014-10-25,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Tae et al.; licensee BioMed Central Ltd.

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