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@ARTICLE{Kranz:834728,
      author       = {Kranz, Angela and Vogel, Alexander and Degner, Ursula and
                      Kiefler, Ines and Bott, Michael and Usadel, Björn and
                      Polen, Tino},
      title        = {{H}igh precision genome sequencing of engineered
                      {G}luconobacter oxydans 621{H} by combining long nanopore
                      and short accurate {I}llumina reads},
      journal      = {Journal of biotechnology},
      volume       = {258},
      issn         = {0168-1656},
      address      = {Amsterdam [u.a.]},
      publisher    = {Elsevier Science},
      reportid     = {FZJ-2017-04627},
      pages        = {197-205},
      year         = {2017},
      note         = {Biotechnologie1},
      abstract     = {State of the art and novel high-throughput DNA sequencing
                      technologies enable fascinating opportunities and
                      applications in the life sciences including microbial
                      genomics. Short high-quality read data already enable not
                      only microbial genome sequencing, yet can be inadequately to
                      solve problems in genome assemblies and for the analysis of
                      structural variants, especially in engineered microbial cell
                      factories. Single-molecule real-time sequencing technologies
                      generating long reads promise to solve such assembly
                      problems. In our study, we wanted to increase the average
                      read length of long nanopore reads with R9 chemistry and
                      conducted a hybrid approach for the analysis of structural
                      variants to check the genome stability of a recombinant
                      Gluconobacter oxydans 621H strain (IK003.1) engineered for
                      improved growth. Therefore we combined accurate Illumina
                      sequencing technology and low-cost single-molecule nanopore
                      sequencing using the MinION® device from Oxford Nanopore.
                      In our hybrid approach with a modified library protocol we
                      could increase the average size of nanopore 2D reads to
                      about 18.9 kb. Combining the long MinION nanopore reads with
                      the high quality short Illumina reads enabled the assembly
                      of the engineered chromosome into a single contig and
                      comprehensive detection and clarification of 7 structural
                      variants including all three known genetically engineered
                      modifications. We found the genome of IK003.1 was stable
                      over 70 generations of strain handling including 28 h of
                      process time in a bioreactor. The long read data revealed a
                      novel 1420 bp transposon-flanked and ORF-containing sequence
                      which was hitherto unknown in the G. oxydans 621H reference.
                      Further analysis and genome sequencing showed that this
                      region is already present in G. oxydans 621H wild-type
                      strains. Our data of G. oxydans 621H wild-type DNA from
                      different resources also revealed in 73 annotated coding
                      sequences about 91 uniform nucleotide differences including
                      InDels. Together, our results contribute to an improved high
                      quality genome reference for G. oxydans 621H which is
                      available via ENA accession PRJEB18739.},
      cin          = {IBG-1 / IBG-2},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IBG-1-20101118 / I:(DE-Juel1)IBG-2-20101118},
      pnm          = {581 - Biotechnology (POF3-581)},
      pid          = {G:(DE-HGF)POF3-581},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:28433722},
      UT           = {WOS:000412611100024},
      doi          = {10.1016/j.jbiotec.2017.04.016},
      url          = {https://juser.fz-juelich.de/record/834728},
}