Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3390/biology7020032 http://hdl.handle.net/11449/171109 |
Resumo: | One 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. |
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Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamicsHPCInpactorLTR retrotransposonsParallel programmingPineappleTransposable elementsOne 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.Department of Electronics and Automatization Universidad Autónoma de ManizalesFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology Fujian Agriculture and Forestry UniversityDepartment of Systems and Informatics Universidad de CaldasDepartment of Botany Instituto de Biociências Universidade Estadual Paulista UNESPDepartment of Biological Sciences Universidad de CaldasDepartment of Plant Biology University of Illinois at Urbana-ChampaignInstitut de Recherche pour le Développement (IRD) CIRAD Université de MontpellierDepartment of Botany Instituto de Biociências Universidade Estadual Paulista UNESPUniversidad Autónoma de ManizalesFujian Agriculture and Forestry UniversityUniversidad de CaldasUniversidade Estadual Paulista (Unesp)University of Illinois at Urbana-ChampaignUniversité de MontpellierOrozco-Arias, SimonLiu, JuanTabares-Soto, ReinelCeballos, DiegoDomingues, Douglas Silva [UNESP]Garavito, AndréaMing, RayGuyot, Romain2018-12-11T16:53:56Z2018-12-11T16:53:56Z2018-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.3390/biology7020032Biology, v. 7, n. 2, 2018.2079-7737http://hdl.handle.net/11449/17110910.3390/biology70200322-s2.0-850486424572-s2.0-85048642457.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBiology1,324info:eu-repo/semantics/openAccess2024-01-09T06:31:10Zoai:repositorio.unesp.br:11449/171109Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-01-09T06:31:10Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
title |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
spellingShingle |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics Orozco-Arias, Simon HPC Inpactor LTR retrotransposons Parallel programming Pineapple Transposable elements |
title_short |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
title_full |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
title_fullStr |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
title_full_unstemmed |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
title_sort |
Inpactor, integrated and parallel analyzer and classifier of LTR retrotransposons and ITS application for pineapple LTR retrotransposons diversity and dynamics |
author |
Orozco-Arias, Simon |
author_facet |
Orozco-Arias, Simon Liu, Juan Tabares-Soto, Reinel Ceballos, Diego Domingues, Douglas Silva [UNESP] Garavito, Andréa Ming, Ray Guyot, Romain |
author_role |
author |
author2 |
Liu, Juan Tabares-Soto, Reinel Ceballos, Diego Domingues, Douglas Silva [UNESP] Garavito, Andréa Ming, Ray Guyot, Romain |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidad Autónoma de Manizales Fujian Agriculture and Forestry University Universidad de Caldas Universidade Estadual Paulista (Unesp) University of Illinois at Urbana-Champaign Université de Montpellier |
dc.contributor.author.fl_str_mv |
Orozco-Arias, Simon Liu, Juan Tabares-Soto, Reinel Ceballos, Diego Domingues, Douglas Silva [UNESP] Garavito, Andréa Ming, Ray Guyot, Romain |
dc.subject.por.fl_str_mv |
HPC Inpactor LTR retrotransposons Parallel programming Pineapple Transposable elements |
topic |
HPC Inpactor LTR retrotransposons Parallel programming Pineapple Transposable elements |
description |
One 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. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T16:53:56Z 2018-12-11T16:53:56Z 2018-01-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3390/biology7020032 Biology, v. 7, n. 2, 2018. 2079-7737 http://hdl.handle.net/11449/171109 10.3390/biology7020032 2-s2.0-85048642457 2-s2.0-85048642457.pdf |
url |
http://dx.doi.org/10.3390/biology7020032 http://hdl.handle.net/11449/171109 |
identifier_str_mv |
Biology, v. 7, n. 2, 2018. 2079-7737 10.3390/biology7020032 2-s2.0-85048642457 2-s2.0-85048642457.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Biology 1,324 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799965572111269888 |