Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina
Background: Deciphering the genetic architecture of drought tolerance could allow the candidate genes identification responding to water stress. In the Andean Patagonian forest, the genus Nothofagus represents an ecologically relevant species to be included in different genomic studies. These studie...
| Autores principales: | , , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer Open
2024
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| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12123/17692 https://ecologicalprocesses.springeropen.com/articles/10.1186/s13717-024-00496-7 https://doi.org/10.1186/s13717-024-00496-7 |
| _version_ | 1855037717847474176 |
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| author | Lopez Laphitz, Rita Maria Arana, María Veronica Varela, Santiago Agustin Becker, Leandro Aníbal Soliani, Carolina Azpilicueta, Maria Marta Marchelli, Paula Bellora, Nicolás |
| author_browse | Arana, María Veronica Azpilicueta, Maria Marta Becker, Leandro Aníbal Bellora, Nicolás Lopez Laphitz, Rita Maria Marchelli, Paula Soliani, Carolina Varela, Santiago Agustin |
| author_facet | Lopez Laphitz, Rita Maria Arana, María Veronica Varela, Santiago Agustin Becker, Leandro Aníbal Soliani, Carolina Azpilicueta, Maria Marta Marchelli, Paula Bellora, Nicolás |
| author_sort | Lopez Laphitz, Rita Maria |
| collection | INTA Digital |
| description | Background: Deciphering the genetic architecture of drought tolerance could allow the candidate genes identification responding to water stress. In the Andean Patagonian forest, the genus Nothofagus represents an ecologically relevant species to be included in different genomic studies. These studies are scarce in South American ecosystems however represent an important source of genomic data in order to interpret future climate-change environment scenarios of these emblematic forests. Here, we achieved the assemblage of the transcriptome of N. alpina while searching for key genes of activated or suppressed metabolic pathways in response to drought stress.
Results: De novo transcriptome assembly resulted in 104,030 transcripts. Following confirmation of drought conditions, based on reduction of leaf water potential and stomatal conductance, a differential gene expression analysis resulted in 2720 significantly expressed genes (1601 up-regulated and 1119 down-regulated). Enrichment analysis (over-representation analysis and gene set enrichment analysis) resulted in more than one hundred stress-responsive term ontologies (i.e. biological processes) and pathways. Terms such as response to abscisic acid and pathways such as plant hormone signal transduction or starch and sucrose metabolism were over-represented. Protein–protein interaction assessment resulted in networks with significantly expressed top common hub gene clusters (e.g. plant-type cell wall biogenesis among down-regulated or ABA-signalling among up-regulated). These networks evidenced important regulators at gene expression such as transcriptional factors.
Conclusions: Responses of N. alpina seedlings to drought stress were evidenced by the activation of several genes linked to GO biological processes and KEGG pathways, which were mainly based on over-expression of specific protein kinases, phosphatases, synthases and transcription factors. This suggests an up-regulation of signalling pathways, triggered through plant hormones such as abscisic acid or auxin, which could counteract the osmotic stress created as a probable immediate response to drought. On the other hand, groups of carbon fixation genes related to the galactose metabolism, photosynthesis, secondary wall biogenesis, and fatty acid biosynthesis degradation were down-regulated under drought. Overall, our results provide new genomic data for understanding how non-model long-lived trees of Patagonian forests would acclimate to environmental changes. |
| format | info:ar-repo/semantics/artículo |
| id | INTA17692 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Springer Open |
| publisherStr | Springer Open |
| record_format | dspace |
| spelling | INTA176922024-05-10T13:47:38Z Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina Lopez Laphitz, Rita Maria Arana, María Veronica Varela, Santiago Agustin Becker, Leandro Aníbal Soliani, Carolina Azpilicueta, Maria Marta Marchelli, Paula Bellora, Nicolás Nothofagus Estrés de Sequia Expresión Génica Cambio Climático Transcriptomas Drought Stress Gene Expression Climate Change Transcriptome Nothofagus alpina Región Patagónica Estrés Hídrico Background: Deciphering the genetic architecture of drought tolerance could allow the candidate genes identification responding to water stress. In the Andean Patagonian forest, the genus Nothofagus represents an ecologically relevant species to be included in different genomic studies. These studies are scarce in South American ecosystems however represent an important source of genomic data in order to interpret future climate-change environment scenarios of these emblematic forests. Here, we achieved the assemblage of the transcriptome of N. alpina while searching for key genes of activated or suppressed metabolic pathways in response to drought stress. Results: De novo transcriptome assembly resulted in 104,030 transcripts. Following confirmation of drought conditions, based on reduction of leaf water potential and stomatal conductance, a differential gene expression analysis resulted in 2720 significantly expressed genes (1601 up-regulated and 1119 down-regulated). Enrichment analysis (over-representation analysis and gene set enrichment analysis) resulted in more than one hundred stress-responsive term ontologies (i.e. biological processes) and pathways. Terms such as response to abscisic acid and pathways such as plant hormone signal transduction or starch and sucrose metabolism were over-represented. Protein–protein interaction assessment resulted in networks with significantly expressed top common hub gene clusters (e.g. plant-type cell wall biogenesis among down-regulated or ABA-signalling among up-regulated). These networks evidenced important regulators at gene expression such as transcriptional factors. Conclusions: Responses of N. alpina seedlings to drought stress were evidenced by the activation of several genes linked to GO biological processes and KEGG pathways, which were mainly based on over-expression of specific protein kinases, phosphatases, synthases and transcription factors. This suggests an up-regulation of signalling pathways, triggered through plant hormones such as abscisic acid or auxin, which could counteract the osmotic stress created as a probable immediate response to drought. On the other hand, groups of carbon fixation genes related to the galactose metabolism, photosynthesis, secondary wall biogenesis, and fatty acid biosynthesis degradation were down-regulated under drought. Overall, our results provide new genomic data for understanding how non-model long-lived trees of Patagonian forests would acclimate to environmental changes. EEA Bariloche Fil: Lopez Laphitz, Rita M. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Diversidad y Evolución Austral; Argentina Fil: Arana, María Veronica. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Arana, María Veronica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Varela, Santiago Agustin. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Varela, Santiago Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Becker, Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Diversidad y Evolución Austral; Argentina Fil: Soliani, Carolina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Soliani, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Azpilicueta, Maria Marta. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Azpilicueta, Maria Marta. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Marchelli, Paula. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Marchelli, Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Tecnologías Nucleares para la Salud; Argentina 2024-05-10T13:31:17Z 2024-05-10T13:31:17Z 2024-05 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://hdl.handle.net/20.500.12123/17692 https://ecologicalprocesses.springeropen.com/articles/10.1186/s13717-024-00496-7 2192-1709 https://doi.org/10.1186/s13717-024-00496-7 eng 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) application/pdf Springer Open Ecological Processes 13 : Article number: 34 (May 2024) |
| spellingShingle | Nothofagus Estrés de Sequia Expresión Génica Cambio Climático Transcriptomas Drought Stress Gene Expression Climate Change Transcriptome Nothofagus alpina Región Patagónica Estrés Hídrico Lopez Laphitz, Rita Maria Arana, María Veronica Varela, Santiago Agustin Becker, Leandro Aníbal Soliani, Carolina Azpilicueta, Maria Marta Marchelli, Paula Bellora, Nicolás Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina |
| title | Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina |
| title_full | Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina |
| title_fullStr | Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina |
| title_full_unstemmed | Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina |
| title_short | Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina |
| title_sort | transcriptomic responses to drought stress in the patagonian southern beech nothofagus alpina |
| topic | Nothofagus Estrés de Sequia Expresión Génica Cambio Climático Transcriptomas Drought Stress Gene Expression Climate Change Transcriptome Nothofagus alpina Región Patagónica Estrés Hídrico |
| url | http://hdl.handle.net/20.500.12123/17692 https://ecologicalprocesses.springeropen.com/articles/10.1186/s13717-024-00496-7 https://doi.org/10.1186/s13717-024-00496-7 |
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