Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis
Background: Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and developme...
| Autores principales: | , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | Inglés |
| Publicado: |
2020
|
| Acceso en línea: | http://hdl.handle.net/20.500.11939/6306 |
| _version_ | 1855032405101903872 |
|---|---|
| author | Sabbione, Agustin Daurelio, Lucas D. Vegetti, Abelardo Talón, Manuel Tadeo, Francisco R. Dotto, Marcela |
| author_browse | Daurelio, Lucas D. Dotto, Marcela Sabbione, Agustin Tadeo, Francisco R. Talón, Manuel Vegetti, Abelardo |
| author_facet | Sabbione, Agustin Daurelio, Lucas D. Vegetti, Abelardo Talón, Manuel Tadeo, Francisco R. Dotto, Marcela |
| author_sort | Sabbione, Agustin |
| collection | ReDivia |
| description | Background: Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and development. Three main gene families are critical components of RNA silencing: DICER-LIKE (DCL), ARGONAUTE (AGO) and RNA-DEPENDENT RNA POLYMERASE (RDR). Even though they have been characterized in other plant species, there is no information about these gene families in Citrus sinensis, one of the most important fruit species from both economical and nutritional reasons. While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet.Results: Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. We characterized their expression patterns in root, leaf, flesh, peel and embryo samples using RNA-seq data. Moreover, we studied their role in fruit abscission through gene expression analysis in fruit rind compared to abscission zone from samples obtained by laser capture microdissection. Interestingly, we determined that the expression of several RNA silencing factors are down-regulated in fruit abscission zone, being particularly represented gene components of the RNA-dependent DNA Methylation pathway, indicating that repression of this process is necessary for fruit abscission to take place in Citrus sinensis.Conclusions: The members of these 3 families present characteristic conserved domains and distinct expression patterns. We provide a detailed analysis of the members of these families and improved the annotation of some of these genes based on RNA-seq data. Our data suggests that the RNA-dependent DNA Methylation pathway is involved in the important fruit abscission process in C. sinensis. |
| format | article |
| id | ReDivia6306 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| record_format | dspace |
| spelling | ReDivia63062025-04-25T14:46:48Z Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis Sabbione, Agustin Daurelio, Lucas D. Vegetti, Abelardo Talón, Manuel Tadeo, Francisco R. Dotto, Marcela Background: Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and development. Three main gene families are critical components of RNA silencing: DICER-LIKE (DCL), ARGONAUTE (AGO) and RNA-DEPENDENT RNA POLYMERASE (RDR). Even though they have been characterized in other plant species, there is no information about these gene families in Citrus sinensis, one of the most important fruit species from both economical and nutritional reasons. While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet.Results: Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. We characterized their expression patterns in root, leaf, flesh, peel and embryo samples using RNA-seq data. Moreover, we studied their role in fruit abscission through gene expression analysis in fruit rind compared to abscission zone from samples obtained by laser capture microdissection. Interestingly, we determined that the expression of several RNA silencing factors are down-regulated in fruit abscission zone, being particularly represented gene components of the RNA-dependent DNA Methylation pathway, indicating that repression of this process is necessary for fruit abscission to take place in Citrus sinensis.Conclusions: The members of these 3 families present characteristic conserved domains and distinct expression patterns. We provide a detailed analysis of the members of these families and improved the annotation of some of these genes based on RNA-seq data. Our data suggests that the RNA-dependent DNA Methylation pathway is involved in the important fruit abscission process in C. sinensis. 2020-02-21T11:51:31Z 2020-02-21T11:51:31Z 2019 article publishedVersion Sabbione, A., Daurelio, L., Vegetti, A., Talon, M., Tadeo, F., & Dotto, M. (2019). Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis. Bmc Plant Biology, 19(1). 1471-2229 http://hdl.handle.net/20.500.11939/6306 10.1186/s12870-019-1998-1 en openAccess electronico |
| spellingShingle | Sabbione, Agustin Daurelio, Lucas D. Vegetti, Abelardo Talón, Manuel Tadeo, Francisco R. Dotto, Marcela Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis |
| title | Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis |
| title_full | Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis |
| title_fullStr | Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis |
| title_full_unstemmed | Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis |
| title_short | Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis |
| title_sort | genome wide analysis of ago dcl and rdr gene families reveals rna directed dna methylation is involved in fruit abscission in citrus sinensis |
| url | http://hdl.handle.net/20.500.11939/6306 |
| work_keys_str_mv | AT sabbioneagustin genomewideanalysisofagodclandrdrgenefamiliesrevealsrnadirecteddnamethylationisinvolvedinfruitabscissionincitrussinensis AT daureliolucasd genomewideanalysisofagodclandrdrgenefamiliesrevealsrnadirecteddnamethylationisinvolvedinfruitabscissionincitrussinensis AT vegettiabelardo genomewideanalysisofagodclandrdrgenefamiliesrevealsrnadirecteddnamethylationisinvolvedinfruitabscissionincitrussinensis AT talonmanuel genomewideanalysisofagodclandrdrgenefamiliesrevealsrnadirecteddnamethylationisinvolvedinfruitabscissionincitrussinensis AT tadeofranciscor genomewideanalysisofagodclandrdrgenefamiliesrevealsrnadirecteddnamethylationisinvolvedinfruitabscissionincitrussinensis AT dottomarcela genomewideanalysisofagodclandrdrgenefamiliesrevealsrnadirecteddnamethylationisinvolvedinfruitabscissionincitrussinensis |