Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum

Autores
Paz, Rosalia Cristina; Kozaczek, Melina Eliana; Rosli, Hernan Guillermo; Andino, Natalia del Pilar; Sánchez Puerta, María Virginia
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.
Fil: Paz, Rosalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; Argentina
Fil: Kozaczek, Melina Eliana. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina
Fil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Fil: Andino, Natalia del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales; Argentina
Fil: Sánchez Puerta, María Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Materia
Expression
Family Delimitation
Full Length Ltr Retroelements
Insertion Time
Phylogeny
Solanum Lycopersicum
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/64879
Acceder
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicumPaz, Rosalia CristinaKozaczek, Melina ElianaRosli, Hernan GuillermoAndino, Natalia del PilarSánchez Puerta, María VirginiaExpressionFamily DelimitationFull Length Ltr RetroelementsInsertion TimePhylogenySolanum Lycopersicumhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.Fil: Paz, Rosalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; ArgentinaFil: Kozaczek, Melina Eliana. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; ArgentinaFil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Andino, Natalia del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales; ArgentinaFil: Sánchez Puerta, María Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; ArgentinaSpringer2017-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/64879Paz, Rosalia Cristina; Kozaczek, Melina Eliana; Rosli, Hernan Guillermo; Andino, Natalia del Pilar; Sánchez Puerta, María Virginia; Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum; Springer; Genetica; 145; 4-5; 10-2017; 417-4300016-6707CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007/s10709-017-9977-7info:eu-repo/semantics/altIdentifier/doi/10.1007/s10709-017-9977-7info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:46:52Zoai:ri.conicet.gov.ar:11336/64879instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:46:53.193CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
title Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
spellingShingle Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
Paz, Rosalia Cristina
Expression
Family Delimitation
Full Length Ltr Retroelements
Insertion Time
Phylogeny
Solanum Lycopersicum
title_short Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
title_full Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
title_fullStr Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
title_full_unstemmed Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
title_sort Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum
dc.creator.none.fl_str_mv Paz, Rosalia Cristina
Kozaczek, Melina Eliana
Rosli, Hernan Guillermo
Andino, Natalia del Pilar
Sánchez Puerta, María Virginia
author Paz, Rosalia Cristina
author_facet Paz, Rosalia Cristina
Kozaczek, Melina Eliana
Rosli, Hernan Guillermo
Andino, Natalia del Pilar
Sánchez Puerta, María Virginia
author_role author
author2 Kozaczek, Melina Eliana
Rosli, Hernan Guillermo
Andino, Natalia del Pilar
Sánchez Puerta, María Virginia
author2_role author
author
author
author
dc.subject.none.fl_str_mv Expression
Family Delimitation
Full Length Ltr Retroelements
Insertion Time
Phylogeny
Solanum Lycopersicum
topic Expression
Family Delimitation
Full Length Ltr Retroelements
Insertion Time
Phylogeny
Solanum Lycopersicum
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.
Fil: Paz, Rosalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan. Centro de Investigaciones de la Geosfera y Biosfera. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones de la Geosfera y Biosfera; Argentina
Fil: Kozaczek, Melina Eliana. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina
Fil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Fil: Andino, Natalia del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales; Argentina
Fil: Sánchez Puerta, María Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
description Transposable elements are the most abundant components of plant genomes and can dramatically induce genetic changes and impact genome evolution. In the recently sequenced genome of tomato (Solanum lycopersicum), the estimated fraction of elements corresponding to retrotransposons is nearly 62%. Given that tomato is one of the most important vegetable crop cultivated and consumed worldwide, understanding retrotransposon dynamics can provide insight into its evolution and domestication processes. In this study, we performed a genome-wide in silico search of full-length LTR retroelements in the tomato nuclear genome and annotated 736 full-length Gypsy and Copia retroelements. The dispersion level across the 12 chromosomes, the diversity and tissue-specific expression of those elements were estimated. Phylogenetic analysis based on the retrotranscriptase region revealed the presence of 12 major lineages of LTR retroelements in the tomato genome. We identified 97 families, of which 77 and 20 belong to the superfamilies Copia and Gypsy, respectively. Each retroelement family was characterized according to their element size, relative frequencies and insertion time. These analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in tomato.
publishDate 2017
dc.date.none.fl_str_mv 2017-10
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/11336/64879
Paz, Rosalia Cristina; Kozaczek, Melina Eliana; Rosli, Hernan Guillermo; Andino, Natalia del Pilar; Sánchez Puerta, María Virginia; Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum; Springer; Genetica; 145; 4-5; 10-2017; 417-430
0016-6707
CONICET Digital
CONICET
url http://hdl.handle.net/11336/64879
identifier_str_mv Paz, Rosalia Cristina; Kozaczek, Melina Eliana; Rosli, Hernan Guillermo; Andino, Natalia del Pilar; Sánchez Puerta, María Virginia; Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum; Springer; Genetica; 145; 4-5; 10-2017; 417-430
0016-6707
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007/s10709-017-9977-7
info:eu-repo/semantics/altIdentifier/doi/10.1007/s10709-017-9977-7
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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