Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Jun 23;256(1):17.
doi: 10.1007/s00425-022-03934-y.

Cultivar-specific miRNA-mediated RNA silencing in grapes

Varsha Tirumalai  1   2 , Anushree Narjala  1   2 , Chenna Swetha  1   2 , G Vivek Hari Sundar  1 , T N Sujith  1 , P V Shivaprasad  3
Affiliations

Cultivar-specific miRNA-mediated RNA silencing in grapes

Varsha Tirumalai et al. Planta. .

Abstract

In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity. However, it is not known if there are variations in miRNA-mediated targeting between subspecies and cultivars that have been subjected to vast genetic modifications through breeding and other selections. Here, we have used PAREsnip2 tool for analysis of degradome datasets derived from two contrasting domesticated grape cultivars having varied fruit color, habit and leaf shape. We identified several interesting variations in sRNA targeting using degradome and 5'RACE analysis between two contrasting grape cultivars that was further correlated using RNA-seq analysis. Several of the differences we identified are associated with secondary metabolic pathways. We propose possible means by which sRNAs might contribute to diversity in secondary metabolites and other development pathways between two domesticated cultivars of grapes.

Keywords: 5’RACE; Degradome analysis; Grapes; Secondary metabolites; miRNAs.

PubMed Disclaimer

References

    1. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets Identified by sequencing of the Arabidopsis degradome. Curr Biol 18:758–762. https://doi.org/10.1016/j.cub.2008.04.042 - DOI - PubMed - PMC
    1. Addo-Quaye C, Miller W, Axtell MJ (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 25:130–131. https://doi.org/10.1093/bioinformatics/btn604 - DOI - PubMed
    1. Ahmed W, Li R, Xia Y et al (2020) Comparative analysis of miRNA expression profiles between heat-tolerant and heat-sensitive genotypes of flowering Chinese cabbage under heat stress using high-throughput sequencing. Genes (basel) 11:264. https://doi.org/10.3390/genes11030264 - DOI
    1. Akbergenov R, Si-Ammour A, Blevins T et al (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34:462–471. https://doi.org/10.1093/nar/gkj447 - DOI - PubMed - PMC
    1. Albert NW, Davies KM, Schwinn KE (2014a) Repression—the dark side of anthocyanin regulation? Acta Hortic 1048:129–136 - DOI

LinkOut - more resources