The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome

Autores
Formey, Damien; Sallet, Erika; Lelandais Brière, Christine; Ben, Cécile; Bustos Sanmamed, Maria del Pilar; Niebel, Andreas; Frugier, Florian; Combier, Jean Philippe; Debellé, Frédéric; Hartmann, Caroline; Poulain, Julie; Gavory, Frédérick; Wincker, Patrick; Roux, Christophe; Gentzbittel, Laurent; Gouzy, Jérôme; Crespi, Martin
Año de publicación
2014
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. Results: In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. Conclusions: We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
Fil: Formey, Damien. Centre National de la Recherche Scientifique; Francia. Université de Toulouse; Francia
Fil: Sallet, Erika. Institut National de la Recherche Agronomique; Francia
Fil: Lelandais Brière, Christine. Université Paris Diderot - Paris 7; Francia
Fil: Ben, Cécile. Université de Toulouse; Francia
Fil: Bustos Sanmamed, Maria del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Université Paris Diderot - Paris 7; Francia
Fil: Niebel, Andreas. Institut National de la Recherche Agronomique; Francia
Fil: Frugier, Florian. Centre National de la Recherche Scientifique; Francia
Fil: Combier, Jean Philippe. Centre National de la Recherche Scientifique; Francia
Fil: Debellé, Frédéric. Institut National de la Recherche Agronomique; Francia
Fil: Hartmann, Caroline. Université Paris Diderot - Paris 7; Francia
Fil: Poulain, Julie. Commissariat A Energie Atomique; Francia
Fil: Gavory, Frédérick. Commissariat A Energie Atomique; Francia
Fil: Wincker, Patrick. Commissariat A Energie Atomique; Francia
Fil: Roux, Christophe. Centre National de la Recherche Scientifique; Francia
Fil: Gentzbittel, Laurent. Université de Toulouse; Francia
Fil: Gouzy, Jérôme. Institut National de la Recherche Agronomique; Francia
Fil: Crespi, Martin. Université Paris Diderot - Paris 7; Francia
Materia
miRNA
Legumes
Abiotic stress
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:11336/94269
Acceder
id CONICETDig_fa75eba35b3a6e6bf4c97e6f2cae7ad2
oai_identifier_str oai:ri.conicet.gov.ar:11336/94269
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAomeFormey, DamienSallet, ErikaLelandais Brière, ChristineBen, CécileBustos Sanmamed, Maria del PilarNiebel, AndreasFrugier, FlorianCombier, Jean PhilippeDebellé, FrédéricHartmann, CarolinePoulain, JulieGavory, FrédérickWincker, PatrickRoux, ChristopheGentzbittel, LaurentGouzy, JérômeCrespi, MartinmiRNALegumesAbiotic stresshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. Results: In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. Conclusions: We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.Fil: Formey, Damien. Centre National de la Recherche Scientifique; Francia. Université de Toulouse; FranciaFil: Sallet, Erika. Institut National de la Recherche Agronomique; FranciaFil: Lelandais Brière, Christine. Université Paris Diderot - Paris 7; FranciaFil: Ben, Cécile. Université de Toulouse; FranciaFil: Bustos Sanmamed, Maria del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Université Paris Diderot - Paris 7; FranciaFil: Niebel, Andreas. Institut National de la Recherche Agronomique; FranciaFil: Frugier, Florian. Centre National de la Recherche Scientifique; FranciaFil: Combier, Jean Philippe. Centre National de la Recherche Scientifique; FranciaFil: Debellé, Frédéric. Institut National de la Recherche Agronomique; FranciaFil: Hartmann, Caroline. Université Paris Diderot - Paris 7; FranciaFil: Poulain, Julie. Commissariat A Energie Atomique; FranciaFil: Gavory, Frédérick. Commissariat A Energie Atomique; FranciaFil: Wincker, Patrick. Commissariat A Energie Atomique; FranciaFil: Roux, Christophe. Centre National de la Recherche Scientifique; FranciaFil: Gentzbittel, Laurent. Université de Toulouse; FranciaFil: Gouzy, Jérôme. Institut National de la Recherche Agronomique; FranciaFil: Crespi, Martin. Université Paris Diderot - Paris 7; FranciaBioMed Central2014-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/94269Formey, Damien; Sallet, Erika; Lelandais Brière, Christine; Ben, Cécile; Bustos Sanmamed, Maria del Pilar; et al.; The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome; BioMed Central; Genome Biology; 15; 9; 9-2014; 457-4571474-760XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-014-0457-4info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0457-4info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:20:18Zoai:ri.conicet.gov.ar:11336/94269instacron: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:34982025-09-29 10:20:18.682CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
title The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
spellingShingle The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
Formey, Damien
miRNA
Legumes
Abiotic stress
title_short The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
title_full The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
title_fullStr The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
title_full_unstemmed The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
title_sort The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
dc.creator.none.fl_str_mv Formey, Damien
Sallet, Erika
Lelandais Brière, Christine
Ben, Cécile
Bustos Sanmamed, Maria del Pilar
Niebel, Andreas
Frugier, Florian
Combier, Jean Philippe
Debellé, Frédéric
Hartmann, Caroline
Poulain, Julie
Gavory, Frédérick
Wincker, Patrick
Roux, Christophe
Gentzbittel, Laurent
Gouzy, Jérôme
Crespi, Martin
author Formey, Damien
author_facet Formey, Damien
Sallet, Erika
Lelandais Brière, Christine
Ben, Cécile
Bustos Sanmamed, Maria del Pilar
Niebel, Andreas
Frugier, Florian
Combier, Jean Philippe
Debellé, Frédéric
Hartmann, Caroline
Poulain, Julie
Gavory, Frédérick
Wincker, Patrick
Roux, Christophe
Gentzbittel, Laurent
Gouzy, Jérôme
Crespi, Martin
author_role author
author2 Sallet, Erika
Lelandais Brière, Christine
Ben, Cécile
Bustos Sanmamed, Maria del Pilar
Niebel, Andreas
Frugier, Florian
Combier, Jean Philippe
Debellé, Frédéric
Hartmann, Caroline
Poulain, Julie
Gavory, Frédérick
Wincker, Patrick
Roux, Christophe
Gentzbittel, Laurent
Gouzy, Jérôme
Crespi, Martin
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv miRNA
Legumes
Abiotic stress
topic miRNA
Legumes
Abiotic stress
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. Results: In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. Conclusions: We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
Fil: Formey, Damien. Centre National de la Recherche Scientifique; Francia. Université de Toulouse; Francia
Fil: Sallet, Erika. Institut National de la Recherche Agronomique; Francia
Fil: Lelandais Brière, Christine. Université Paris Diderot - Paris 7; Francia
Fil: Ben, Cécile. Université de Toulouse; Francia
Fil: Bustos Sanmamed, Maria del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Université Paris Diderot - Paris 7; Francia
Fil: Niebel, Andreas. Institut National de la Recherche Agronomique; Francia
Fil: Frugier, Florian. Centre National de la Recherche Scientifique; Francia
Fil: Combier, Jean Philippe. Centre National de la Recherche Scientifique; Francia
Fil: Debellé, Frédéric. Institut National de la Recherche Agronomique; Francia
Fil: Hartmann, Caroline. Université Paris Diderot - Paris 7; Francia
Fil: Poulain, Julie. Commissariat A Energie Atomique; Francia
Fil: Gavory, Frédérick. Commissariat A Energie Atomique; Francia
Fil: Wincker, Patrick. Commissariat A Energie Atomique; Francia
Fil: Roux, Christophe. Centre National de la Recherche Scientifique; Francia
Fil: Gentzbittel, Laurent. Université de Toulouse; Francia
Fil: Gouzy, Jérôme. Institut National de la Recherche Agronomique; Francia
Fil: Crespi, Martin. Université Paris Diderot - Paris 7; Francia
description Background: Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. Results: In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. Conclusions: We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
publishDate 2014
dc.date.none.fl_str_mv 2014-09
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/11336/94269
Formey, Damien; Sallet, Erika; Lelandais Brière, Christine; Ben, Cécile; Bustos Sanmamed, Maria del Pilar; et al.; The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome; BioMed Central; Genome Biology; 15; 9; 9-2014; 457-457
1474-760X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/94269
identifier_str_mv Formey, Damien; Sallet, Erika; Lelandais Brière, Christine; Ben, Cécile; Bustos Sanmamed, Maria del Pilar; et al.; The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome; BioMed Central; Genome Biology; 15; 9; 9-2014; 457-457
1474-760X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-014-0457-4
info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0457-4
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
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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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score 13.070432

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