Complete nucleotide sequence of a new filamentous phage, Xf109, which integrates its genome into the chromosomal DNA of Xanthomonas oryzae

Arch Virol. 2017 Feb;162(2):567-572. doi: 10.1007/s00705-016-3105-3. Epub 2016 Oct 14.


Unlike Ff-like coliphages, certain filamentous Inoviridae phages integrate their genomes into the host chromosome and enter a prophage state in their infectious cycle. This lysogenic life cycle was first reported for Xanthomonas citri Cf phage. However, except for the X. citri phages Cf and XacF1, complete genome sequence information about lysogenic Xanthomonas phages is not available to date. A proviral sequence of Xf109 phage was identified in the genome of Xanthomonas oryzae, the rice bacterial blight pathogen, and revived as infectious virions to lysogenize its host de novo. The genome of Xf109 phage is 7190 nucleotides in size and contains 12 predicted open reading frames in an organization similar to that of the Cf phage genome. Seven of the Xf109 proteins show significant sequence similarity to Cf and XacF1 phage proteins, while its ORF4 shares 92 % identity with the major coat protein of X. phage oryzae Xf. Integration of Xf109 phage DNA into the host genome is site-specific, and the attP/attB sequence contains the dif core sequence 5'-TATACATTATGCGAA-3', which is identical to that of Cf, XacF1, and Xanthomonas campestris phage ϕLf. To my knowledge, this is the first complete genome sequence of a filamentous bacteriophage that infects X. oryzae.

MeSH terms

  • Base Sequence
  • Capsid Proteins / genetics
  • Chromosome Mapping
  • Chromosomes, Bacterial / chemistry*
  • DNA, Viral / genetics*
  • Gene Expression
  • Genome, Viral*
  • Inovirus / genetics*
  • Inovirus / isolation & purification
  • Lysogeny
  • Mutagenesis, Insertional*
  • Open Reading Frames
  • Oryza / microbiology
  • Sequence Alignment
  • Virion / genetics
  • Xanthomonas / virology*


  • Capsid Proteins
  • DNA, Viral