Sequencing of E. coli strain UTI89 on multiple sequencing platforms
Fenlon, S.N. Chee, Y.C. Chee, J.L.Y. Choy, Y.H. Khng, A.J. Liow, L.T. Mehershahi, K.S. Ruan, X. Turner, S.W. Yao, F.
Fenlon, S.N.
Chee, J.L.Y.
Choy, Y.H.
Khng, A.J.
Ruan, X.
Turner, S.W.
Yao, F.
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Alternative Title
Abstract
Objectives: The availability of matched sequencing data for the same sample across different sequencing platforms is a necessity for validation and effective comparison of sequencing platforms. A commonly sequenced sample is the lab-adapted MG1655 strain of Escherichia coli; however, this strain is not fully representative of more complex and dynamic genomes of pathogenic E. coli strains. Data description: We present six new sequencing data sets for another E. coli strain, UTI89, which is an extraintestinal pathogenic strain isolated from a patient suffering from a urinary tract infection. We now provide matched whole genome sequencing data generated using the PacBio RSII, Oxford Nanopore MinION R9.4, Ion Torrent, ABI SOLiD, and Illumina NextSeq sequencers. Together with other publically available datasets, UTI89 has a nearly complete suite of data generated on most second- and third-generation sequencers. These data can be used as an additional validation set for new sequencing technologies and analytical methods. More than being another E. coli strain, however, UTI89 is pathogenic, with a 10% larger genome, additional pathogenicity islands, and a large plasmid, features that are common among other naturally occurring and disease-causing E. coli isolates. These data therefore provide a more medically relevant test set for development of algorithms. © 2020, The Author(s).
Keywords
Escherichia coli, Illumina, Ion Torrent, MinION, Oxford Nanopore, PacBio, Roche454, SOLiD, UPEC, Urinary Tract Infection (UTI)
Source Title
BMC Research Notes
Publisher
BioMed Central Ltd
Series/Report No.
Collections
Rights
Attribution 4.0 International
Date
2020
DOI
10.1186/s13104-020-05335-4
Type
Article