Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution

Autores
Zavallo, Diego; Cara, Nicolás; Leone, Melisa; Crescente, Juan Manuel; Marfil, Carlos Federico; Masuelli, Ricardo Williams; Asurmendi, Sebastian
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic “shock” that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
Instituto de Biotecnología
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Cara, Nicolás. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Cara, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Leone, Melisa. Universidad Nacional de Hurlingham, Instituto de Biotecnología; Argentina
Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina
Fil: Marfil, Carlos Federico. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Masuelli, Ricardo Williams. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Masuelli, Ricardo Williams. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
Plant Cell Reports 43 (4) : 85 (April 2024)
Materia
Ribonucleases
Diploidy
Hybrids
RNA
Ribonucleasas
Solanum tuberosum
Diploidia
Híbridos
ARN
Solanum kurtzianum
Regulación Transcripcional
Alopoliploidización
Transcriptional Regulation
Allopolyploidization
Nivel de accesibilidad
acceso restringido
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:20.500.12123/18231
Acceder
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oai_identifier_str oai:localhost:20.500.12123/18231
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distributionZavallo, DiegoCara, NicolásLeone, MelisaCrescente, Juan ManuelMarfil, Carlos FedericoMasuelli, Ricardo WilliamsAsurmendi, SebastianRibonucleasesDiploidyHybridsRNARibonucleasasSolanum tuberosumDiploidiaHíbridosARNSolanum kurtzianumRegulación TranscripcionalAlopoliploidizaciónTranscriptional RegulationAllopolyploidizationAllopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic “shock” that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.Instituto de BiotecnologíaFil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cara, Nicolás. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; ArgentinaFil: Cara, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Leone, Melisa. Universidad Nacional de Hurlingham, Instituto de Biotecnología; ArgentinaFil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; ArgentinaFil: Marfil, Carlos Federico. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Masuelli, Ricardo Williams. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; ArgentinaFil: Masuelli, Ricardo Williams. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); ArgentinaFil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaSpringer2024-06-24T09:53:12Z2024-06-24T09:53:12Z2024-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/18231https://link.springer.com/article/10.1007/s00299-024-03170-61432-203Xhttps://doi.org/10.1007/s00299-024-03170-6Plant Cell Reports 43 (4) : 85 (April 2024)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2019-PD-E6-I116-001, Identificación y análisis funcional de genes o redes génicas de interés biotecnológico con fin agropecuario, forestal, agroalimentario y/o agroindustrialinfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-04T09:50:27Zoai:localhost:20.500.12123/18231instacron: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 09:50:27.516INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
title Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
spellingShingle Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
Zavallo, Diego
Ribonucleases
Diploidy
Hybrids
RNA
Ribonucleasas
Solanum tuberosum
Diploidia
Híbridos
ARN
Solanum kurtzianum
Regulación Transcripcional
Alopoliploidización
Transcriptional Regulation
Allopolyploidization
title_short Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
title_full Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
title_fullStr Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
title_full_unstemmed Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
title_sort Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
dc.creator.none.fl_str_mv Zavallo, Diego
Cara, Nicolás
Leone, Melisa
Crescente, Juan Manuel
Marfil, Carlos Federico
Masuelli, Ricardo Williams
Asurmendi, Sebastian
author Zavallo, Diego
author_facet Zavallo, Diego
Cara, Nicolás
Leone, Melisa
Crescente, Juan Manuel
Marfil, Carlos Federico
Masuelli, Ricardo Williams
Asurmendi, Sebastian
author_role author
author2 Cara, Nicolás
Leone, Melisa
Crescente, Juan Manuel
Marfil, Carlos Federico
Masuelli, Ricardo Williams
Asurmendi, Sebastian
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Ribonucleases
Diploidy
Hybrids
RNA
Ribonucleasas
Solanum tuberosum
Diploidia
Híbridos
ARN
Solanum kurtzianum
Regulación Transcripcional
Alopoliploidización
Transcriptional Regulation
Allopolyploidization
topic Ribonucleases
Diploidy
Hybrids
RNA
Ribonucleasas
Solanum tuberosum
Diploidia
Híbridos
ARN
Solanum kurtzianum
Regulación Transcripcional
Alopoliploidización
Transcriptional Regulation
Allopolyploidization
dc.description.none.fl_txt_mv Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic “shock” that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
Instituto de Biotecnología
Fil: Zavallo, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Zavallo, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Cara, Nicolás. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Cara, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Leone, Melisa. Universidad Nacional de Hurlingham, Instituto de Biotecnología; Argentina
Fil: Crescente, Juan Manuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Marcos Juárez. Grupo Biotecnología y Recursos Genéticos; Argentina
Fil: Marfil, Carlos Federico. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Masuelli, Ricardo Williams. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Masuelli, Ricardo Williams. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Asurmendi, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina
Fil: Asurmendi, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic “shock” that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
publishDate 2024
dc.date.none.fl_str_mv 2024-06-24T09:53:12Z
2024-06-24T09:53:12Z
2024-04
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/20.500.12123/18231
https://link.springer.com/article/10.1007/s00299-024-03170-6
1432-203X
https://doi.org/10.1007/s00299-024-03170-6
url http://hdl.handle.net/20.500.12123/18231
https://link.springer.com/article/10.1007/s00299-024-03170-6
https://doi.org/10.1007/s00299-024-03170-6
identifier_str_mv 1432-203X
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2019-PD-E6-I116-001, Identificación y análisis funcional de genes o redes génicas de interés biotecnológico con fin agropecuario, forestal, agroalimentario y/o agroindustrial
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
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 restrictedAccess
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 Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv Plant Cell Reports 43 (4) : 85 (April 2024)
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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