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Microbiologyopen. 2017 Aug;6(4). doi: 10.1002/mbo3.465. Epub 2017 Mar 27.

Revision and reannotation of the Halomonas elongata DSM 2581T genome.

Author information

1
Computational Biology Group, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
2
Research and Development Division, bitop AG, Witten, Germany.
3
Materials and Environment Division, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.
4
Faculty of Mechanical Engineering, Specialty Division for Systems Biotechnology, Technische Universität München, Germany.
5
Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany.

Abstract

The genome of the Halomonas elongata type strain DSM 2581, an industrial producer, was reevaluated using the Illumina HiSeq2500 technology. To resolve duplication-associated ambiguities, PCR products were generated and sequenced. Outside of duplications, 72 sequence corrections were required, of which 24 were point mutations and 48 were indels of one or few bases. Most of these were associated with polynucleotide stretches (poly-T stretch overestimated in 19 cases, poly-C underestimated in 15 cases). These problems may be attributed to using 454 technology for original genome sequencing. On average, the original genome sequence had only one error in 56 kb. There were 23 frameshift error corrections in the 29 protein-coding genes affected by sequence revision. The genome has been subjected to major reannotation in order to substantially increase the annotation quality.

KEYWORDS:

Halomonas elongata; frameshift; genome annotation; genome sequencing; halophilic bacteria; sequence revision

PMID:
28349658
PMCID:
PMC5552945
DOI:
10.1002/mbo3.465
[Indexed for MEDLINE]
Free PMC Article

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