MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes

Autores
Crescente, Juan Manuel; Zavallo, Diego; Helguera, Marcelo; Vanzetti, Leonardo Sebastian
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
EEA Marcos Juárez
Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina
Fil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
BMC bioinformatics 19 : 348. (2018)
Materia
Arroz
Trigo
Triticum Aestivum
Oryza Sativa
Genomas
Transposones
Rice
Wheat
Genomes
Transposons
Transposable Element
MITE
Miniature Inverted-repeat Transposable Elements
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/3607
Acceder
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oai_identifier_str oai:localhost:20.500.12123/3607
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomesCrescente, Juan ManuelZavallo, DiegoHelguera, MarceloVanzetti, Leonardo SebastianArrozTrigoTriticum AestivumOryza SativaGenomasTransposonesRiceWheatGenomesTransposonsTransposable ElementMITEMiniature Inverted-repeat Transposable ElementsBackground: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.EEA Marcos JuárezFil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; ArgentinaFil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaBioMed Central2018-10-17T12:33:16Z2018-10-17T12:33:16Z2018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/3607https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y1471-2105https://doi.org/10.1186/s12859-018-2376-yBMC bioinformatics 19 : 348. (2018)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-04T09:47:37Zoai:localhost:20.500.12123/3607instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:47:37.949INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
spellingShingle MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
Crescente, Juan Manuel
Arroz
Trigo
Triticum Aestivum
Oryza Sativa
Genomas
Transposones
Rice
Wheat
Genomes
Transposons
Transposable Element
MITE
Miniature Inverted-repeat Transposable Elements
title_short MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_full MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_fullStr MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_full_unstemmed MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
title_sort MITE Tracker : an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
dc.creator.none.fl_str_mv Crescente, Juan Manuel
Zavallo, Diego
Helguera, Marcelo
Vanzetti, Leonardo Sebastian
author Crescente, Juan Manuel
author_facet Crescente, Juan Manuel
Zavallo, Diego
Helguera, Marcelo
Vanzetti, Leonardo Sebastian
author_role author
author2 Zavallo, Diego
Helguera, Marcelo
Vanzetti, Leonardo Sebastian
author2_role author
author
author
dc.subject.none.fl_str_mv Arroz
Trigo
Triticum Aestivum
Oryza Sativa
Genomas
Transposones
Rice
Wheat
Genomes
Transposons
Transposable Element
MITE
Miniature Inverted-repeat Transposable Elements
topic Arroz
Trigo
Triticum Aestivum
Oryza Sativa
Genomas
Transposones
Rice
Wheat
Genomes
Transposons
Transposable Element
MITE
Miniature Inverted-repeat Transposable Elements
dc.description.none.fl_txt_mv Background: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
EEA Marcos Juárez
Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Helguera, Marcelo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina
Fil: Vanzetti, Leonardo Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Background: Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. Results: Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. Conclusions: Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
publishDate 2018
dc.date.none.fl_str_mv 2018-10-17T12:33:16Z
2018-10-17T12:33:16Z
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/3607
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y
1471-2105
https://doi.org/10.1186/s12859-018-2376-y
url http://hdl.handle.net/20.500.12123/3607
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2376-y
https://doi.org/10.1186/s12859-018-2376-y
identifier_str_mv 1471-2105
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv BMC bioinformatics 19 : 348. (2018)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.623145

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