title: Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi.
abstract: BACKGROUND
  Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species.
  
  
  RESULTS
  Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons.
  
  
  CONCLUSIONS
  P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.
authors.forename: Raúl
authors.initials: R
authors.lastname: Castanera
authors.forename: Gúmer
authors.initials: G
authors.lastname: Pérez
authors.forename: Leticia
authors.initials: L
authors.lastname: López
authors.forename: Rubén
authors.initials: R
authors.lastname: Sancho
authors.forename: Francisco
authors.initials: F
authors.lastname: Santoyo
authors.forename: Manuel
authors.initials: M
authors.lastname: Alfaro
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.forename: Antonio G
authors.initials: AG
authors.lastname: Pisabarro
authors.forename: José A
authors.initials: JA
authors.lastname: Oguiza
authors.affiliation: Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, 31006 Pamplona, Navarre, Spain. lramirez@unavarra.es.
authors.forename: Lucía
authors.initials: L
authors.lastname: Ramírez
mesh_terms: D001483:Base Sequence; D004265:DNA Helicases / Q000145:classification / Q000235:genetics / Q000378:metabolism; D004251:DNA Transposable Elements / Q000235:genetics*; D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D010802:Phylogeny; D020076:Pleurotus / Q000235:genetics*; D017434:Protein Structure, Tertiary; D018626:Retroelements / Q000235:genetics; D016415:Sequence Alignment; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements; D005656:Fungal Proteins; D018626:Retroelements; D004265:DNA Helicases