Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi

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• dc.contributor.author Castanera, Raúlca
• dc.contributor.author Pérez, Gúmerca
• dc.contributor.author López, Leticiaca
• dc.contributor.author Sancho, Rubénca
• dc.contributor.author Santoyo, Franciscoca
• dc.contributor.author Alfaro, Manuelca
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
• dc.contributor.author Pisabarro, Antonio Gca
• dc.contributor.author Oguiza, José A.ca
• dc.contributor.author Ramírez, Lucíaca
• dc.date.accessioned 2015-03-25T10:43:34Z
• dc.date.available 2015-03-25T10:43:34Z
• dc.date.issued 2014ca
• dc.description.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. Conclusion: 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.en
• dc.description.sponsorship This work was supported by funds from the AGL2011-30495 project of the Spanish National Research Plan and by additional institutional support from the Public University of Navarreen
• dc.format.mimetype application/pdfca
• dc.identifier.citation Castanera R, Pérez G, López L, Sancho R, Santoyo F, Alfaro M et al. Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics. 2014; 15: 1071. DOI 10.1186/1471-2164-15-1071ca
• dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-15-1071
• dc.identifier.issn 1471-2164ca
• dc.identifier.uri http://hdl.handle.net/10230/23274
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof BMC Genomics. 2014; 15: 1071
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/AGL2011-30495
• dc.rights © 2014 Castanera et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0
• dc.subject.keyword Helitronen
• dc.subject.keyword Transposable elementen
• dc.subject.keyword Gene expressionen
• dc.subject.keyword Gene captureen
• dc.subject.keyword Pleurotus ostreatusen
• dc.subject.keyword Helicaseen
• dc.subject.keyword Basidiomyceteen
• dc.subject.keyword Genome structureen
• dc.subject.other Genòmicaca
• dc.subject.other Genètica vegetalca
• dc.title Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungien
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca