title: Non-canonical Helitrons inFusarium oxysporum.
abstract: BACKGROUND
  Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi.
  
  
  RESULTS
  Here, we comprehensively survey Helitrons in several completely sequenced genomes representing theF. oxysporumspecies complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics.
  
  
  CONCLUSIONS
  FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.
authors.affiliation: Department of Computational Biology and Bioinformatics, University of Kerala, Karyavattom Campus, Karyavattom PO, Trivandrum, Kerala India ; Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands.
authors.forename: Biju Vadakkemukadiyil
authors.initials: BV
authors.lastname: Chellapan
authors.affiliation: Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: van Dam
authors.affiliation: Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Rep
authors.affiliation: Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands.
authors.forename: Ben J C
authors.initials: BJ
authors.lastname: Cornelissen
authors.affiliation: Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands.
authors.forename: Like
authors.initials: L
authors.lastname: Fokkens
keywords: Fusarium oxysporum; Helentrons; Helitron2; Helitrons; Rolling circle; Terminal inverted repeats; Transposon