Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution
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 occasi...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Artículo |
| Language: | Inglés |
| Published: |
Springer
2024
|
| Subjects: | |
| Online Access: | 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 |
| _version_ | 1855486130556764160 |
|---|---|
| author | Zavallo, Diego Cara, Nicolás Leone, Melisa Crescente, Juan Manuel Marfil, Carlos Federico Masuelli, Ricardo Williams Asurmendi, Sebastian |
| author_browse | Asurmendi, Sebastian Cara, Nicolás Crescente, Juan Manuel Leone, Melisa Marfil, Carlos Federico Masuelli, Ricardo Williams Zavallo, Diego |
| author_facet | Zavallo, Diego Cara, Nicolás Leone, Melisa Crescente, Juan Manuel Marfil, Carlos Federico Masuelli, Ricardo Williams Asurmendi, Sebastian |
| author_sort | Zavallo, Diego |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA18231 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA182312024-06-24T10:15:23Z Assessing small RNA profles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution Zavallo, Diego Cara, Nicolás Leone, Melisa Crescente, Juan Manuel Marfil, Carlos Federico Masuelli, Ricardo Williams Asurmendi, Sebastian Ribonucleases Diploidy Hybrids RNA Ribonucleasas Solanum tuberosum Diploidia Híbridos ARN Solanum kurtzianum Regulación Transcripcional Alopoliploidización Transcriptional Regulation Allopolyploidization 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 2024-06-24T09:53:12Z 2024-06-24T09:53:12Z 2024-04 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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 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) application/pdf Springer Plant Cell Reports 43 (4) : 85 (April 2024) |
| spellingShingle | Ribonucleases Diploidy Hybrids RNA Ribonucleasas Solanum tuberosum Diploidia Híbridos ARN Solanum kurtzianum Regulación Transcripcional Alopoliploidización Transcriptional Regulation Allopolyploidization Zavallo, Diego Cara, Nicolás Leone, Melisa Crescente, Juan Manuel Marfil, Carlos Federico Masuelli, Ricardo Williams Asurmendi, Sebastian 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 |
| 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_short | 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 |
| topic | Ribonucleases Diploidy Hybrids RNA Ribonucleasas Solanum tuberosum Diploidia Híbridos ARN Solanum kurtzianum Regulación Transcripcional Alopoliploidización Transcriptional Regulation Allopolyploidization |
| 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 |
| work_keys_str_mv | AT zavallodiego assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution AT caranicolas assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution AT leonemelisa assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution AT crescentejuanmanuel assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution AT marfilcarlosfederico assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution AT masuelliricardowilliams assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution AT asurmendisebastian assessingsmallrnaproflesinpotatodiploidhybridanditsresynthesizedallopolyploidrevealsconservedabundancewithdistinctgenomicdistribution |