Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

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dc.contributor.authorCastanera Andrés, Raúl
dc.contributor.authorPérez Garrido, María Gumersinda
dc.contributor.authorLópez Varas, Leticia
dc.contributor.authorAmselem, Joëlle
dc.contributor.authorLaButti, Kurt
dc.contributor.authorSingan, Vasanth
dc.contributor.authorLipzen, Anna
dc.contributor.authorHaridas, Sajeet
dc.contributor.authorBarry, Kerrie
dc.contributor.authorGrigoriev, Igor V.
dc.contributor.authorPisabarro de Lucas, Gerardo
dc.contributor.authorRamírez Nasto, Lucía
dc.contributor.departmentProducción Agrariaes_ES
dc.contributor.departmentNekazaritza Ekoizpenaeu
dc.contributor.funderUniversidad Pública de Navarra / Nafarroako Unibertsitate Publikoaes
dc.date.accessioned2018-08-31T08:07:59Z
dc.date.available2018-08-31T08:07:59Z
dc.date.issued2017
dc.description.abstractBackground: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. Results: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTRretrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years. Conclusions: Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species.en
dc.description.sponsorshipThis work was supported by Spanish National Research Plan (Project AGL2014–55971-R) and FEDER funds; Public University of Navarre. The work of RC is supported by an FPI grant from the Spanish Ministry of Economy and Competitiveness. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.en
dc.format.extent14 p.
dc.format.mimetypeapplication/pdfen
dc.format.mimetypeapplication/zipen
dc.identifier.doi10.1186/s12864-017-4243-z
dc.identifier.issn1471-2164
dc.identifier.urihttps://academica-e.unavarra.es/handle/2454/30353
dc.language.isoengen
dc.publisherBioMed Centralen
dc.relation.ispartofBMC Genomics (2017) 18:883en
dc.relation.projectIDinfo:eu-repo/grantAgreement/MINECO//AGL2014-55971-R/ES/
dc.relation.publisherversionhttps://doi.org/10.1186/s12864-017-4243-z
dc.rights© The Author(s). 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.en
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectBoletalesen
dc.subjectBrown-roten
dc.subjectBasidiomyceteen
dc.subjectGenomeen
dc.subjectAnnotationen
dc.subjectTransposable elementsen
dc.subjectRetrotransposonen
dc.titleComparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletalesen
dc.typeinfo:eu-repo/semantics/article
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dspace.entity.typePublication
relation.isAuthorOfPublication37776e2e-4a19-49fa-86d2-8691c240f2ad
relation.isAuthorOfPublication42c7e5c5-03c4-4a68-9f3f-06c1301753c0
relation.isAuthorOfPublicationfcf7c03b-9806-45b2-ba35-eed9e1d695d6
relation.isAuthorOfPublication54daf1c4-f273-4ade-a90e-7df28e761ca7
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relation.isAuthorOfPublication.latestForDiscovery37776e2e-4a19-49fa-86d2-8691c240f2ad

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