Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics

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dc.contributor.authorOrozco-Arias, Simon
dc.contributor.authorLiu, Juan
dc.contributor.authorTabares-Soto, Reinel
dc.contributor.authorCeballos, Diego
dc.contributor.authorDomingues, Douglas Silva [UNESP]
dc.contributor.authorGaravito, Andréa
dc.contributor.authorMing, Ray
dc.contributor.authorGuyot, Romain
dc.contributor.institutionUniversidad Autónoma de Manizales
dc.contributor.institutionFujian Agriculture and Forestry University
dc.contributor.institutionUniversidad de Caldas
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionUniversity of Illinois at Urbana-Champaign
dc.contributor.institutionUniversité de Montpellier
dc.date.accessioned2018-12-11T16:53:56Z
dc.date.available2018-12-11T16:53:56Z
dc.date.issued2018-01-01
dc.description.abstractOne particular class of Transposable Elements (TEs), called Long Terminal Repeats (LTRs), retrotransposons, comprises the most abundant mobile elements in plant genomes. Their copy number can vary from several hundreds to up to a few million copies per genome, deeply affecting genome organization and function. The detailed classification of LTR retrotransposons is an essential step to precisely understand their effect at the genome level, but remains challenging in large-sized genomes, requiring the use of optimized bioinformatics tools that can take advantage of supercomputers. Here, we propose a new tool: Inpactor, a parallel and scalable pipeline designed to classify LTR retrotransposons, to identify autonomous and non-autonomous elements, to perform RT-based phylogenetic trees and to analyze their insertion times using High Performance Computing (HPC) techniques. Inpactor was tested on the classification and annotation of LTR retrotransposons in pineapple, a recently-sequenced genome. The pineapple genome assembly comprises 44% of transposable elements, of which 23% were classified as LTR retrotransposons. Exceptionally, 16.4% of the pineapple genome assembly corresponded to only one lineage of the Gypsy superfamily: Del, suggesting that this particular lineage has undergone a significant increase in its copy numbers. As demonstrated for the pineapple genome, Inpactor provides comprehensive data of LTR retrotransposons’ classification and dynamics, allowing a fine understanding of their contribution to genome structure and evolution. Inpactor is available at https://github.com/simonorozcoarias/Inpactor.en
dc.description.affiliationDepartment of Electronics and Automatization Universidad Autónoma de Manizales
dc.description.affiliationFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology Fujian Agriculture and Forestry University
dc.description.affiliationDepartment of Systems and Informatics Universidad de Caldas
dc.description.affiliationDepartment of Botany Instituto de Biociências Universidade Estadual Paulista UNESP
dc.description.affiliationDepartment of Biological Sciences Universidad de Caldas
dc.description.affiliationDepartment of Plant Biology University of Illinois at Urbana-Champaign
dc.description.affiliationInstitut de Recherche pour le Développement (IRD) CIRAD Université de Montpellier
dc.description.affiliationUnespDepartment of Botany Instituto de Biociências Universidade Estadual Paulista UNESP
dc.identifierhttp://dx.doi.org/10.3390/biology7020032
dc.identifier.citationBiology, v. 7, n. 2, 2018.
dc.identifier.doi10.3390/biology7020032
dc.identifier.file2-s2.0-85048642457.pdf
dc.identifier.issn2079-7737
dc.identifier.scopus2-s2.0-85048642457
dc.identifier.urihttp://hdl.handle.net/11449/171109
dc.language.isoeng
dc.relation.ispartofBiology
dc.relation.ispartofsjr1,324
dc.rights.accessRightsAcesso aberto
dc.sourceScopus
dc.subjectHPC
dc.subjectInpactor
dc.subjectLTR retrotransposons
dc.subjectParallel programming
dc.subjectPineapple
dc.subjectTransposable elements
dc.titleInpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamicsen
dc.typeArtigo

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