Abstract
BackgroundSmall 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.ResultsUsing 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.ConclusionsThe 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.
Highlights
Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response
We established that selected members of these families as well as additional single copy factors of the RNAdependent DNA methylation (RdDM) pathway show differential expression in the fruit abscission zone of sweet orange samples analyzed using laser capture microdissection (LCM)
The characteristics of all the genes identified in this study are detailed in Table 1, including gene IDs in both databases, ORF length, protein length, isoelectric point (IP) and molecular weight (Mw), while the gene structure analysis and the updated protein sequences for the corrected gene structural annotations are detailed in Additional file 2
Summary
Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. 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. The biogenesis and action of these regulatory molecules depend mainly on members of the AGO, RDR and DCL families. A total of 20 genes coding for these protein families have been identified in Arabidopsis, 28 genes in tomato and maize [5, 9], 32 genes in rice [3] and 22 in grapevine and pepper [10, 11]
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