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@ARTICLE{Sharma:1005578,
      author       = {Sharma, Vikas and Hünnefeld, Max and Luthe, Tom and
                      Frunzke, Julia},
      title        = {{S}ystematic analysis of prophage elements in
                      actinobacterial genomes reveals a remarkable phylogenetic
                      diversity},
      journal      = {Scientific reports},
      volume       = {13},
      number       = {1},
      issn         = {2045-2322},
      address      = {[London]},
      publisher    = {Macmillan Publishers Limited, part of Springer Nature},
      reportid     = {FZJ-2023-01539},
      pages        = {4410},
      year         = {2023},
      note         = {IBT-1},
      abstract     = {Actinobacteria represent one of the largest bacterial phyla
                      harboring many species of high medical, biotechnological and
                      ecological relevance. Prophage elements are major
                      contributors to bacterial genome diversity and were shown to
                      significantly shape bacterial fitness and host-microbe
                      interactions. In this study, we performed a systematic
                      analysis of prophage elements in 2406 complete
                      actinobacterial genomes. Overall, 2106 prophage elements
                      were predicted to be present in about $50\%$ (1172/2406) of
                      the analyzed datasets. Interestingly, these identified
                      sequences compose a high prevalence of cryptic prophage
                      elements, indicating genetic decay and domestication.
                      Analysis of the sequence relationship of predicted prophages
                      with known actinobacteriophage genomes revealed an
                      exceptional high phylogenetic diversity of prophage
                      elements. As a trend, we observed a higher prevalence of
                      prophage elements in vicinity to the terminus. Analysis of
                      the prophage-encoded gene functions revealed that prophage
                      sequences significantly contribute to the bacterial
                      antiviral immune system, but no biosynthetic gene clusters
                      involved in the synthesis of known antiphage molecules were
                      identified in prophage genomes. Overall, the current study
                      highlights the remarkable diversity of prophages in
                      actinobacterial genomes, with highly divergent prophages in
                      actinobacterial genomes and thus provides an important basis
                      for further investigation of phage-host interactions in this
                      important bacterial phylum.},
      cin          = {IBG-1},
      ddc          = {600},
      cid          = {I:(DE-Juel1)IBG-1-20101118},
      pnm          = {2171 - Biological and environmental resources for
                      sustainable use (POF4-217)},
      pid          = {G:(DE-HGF)POF4-2171},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {36932119},
      UT           = {WOS:000955841200051},
      doi          = {10.1038/s41598-023-30829-z},
      url          = {https://juser.fz-juelich.de/record/1005578},
}