Abstract
Main conclusion
In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting.
Abstract
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.
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Data availability
sRNA sequencing data for BB and DK grapes are available in Gene Expression Omnibus (GEO) series GSE107907, from GSM2883166 to GSM2883177 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107907). RNA sequencing data are available in GEO series GSE107905, from GSM2883154 to GSM2883165 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107905). Degradome data are available in GSE118701 series (from GSM3336816 to GSM333619) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118701). The datasets used for analysis in our current study were from our previous study (Tirumalai et al. 2019).
Abbreviations
- BB:
-
Grape cv Bangalore Blue
- DK:
-
Grape cv Dilkhush
- PhasiRNAs:
-
Phased siRNAs
- RACE:
-
Rapid amplification of cDNA ends
- TasiRNAs:
-
Transacting siRNAs
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Acknowledgements
The authors acknowledge Genotypic Technologies, Bangalore for sRNA and RNA-seq. Thanks to Dr. Awadhesh Pandit, NGS facility, NCBS for performing the degradome sequencing.
Funding
PVS lab is supported by NCBS-TIFR core funding and grants (BT/PR12394/AGIII/103/891/2014; BT/IN/Swiss/47/JGK/2018–19; BT/PR25767/GET/ 119/151/2017) from Department of Biotechnology, Government of India. We also acknowledge support of the Department of Atomic Energy, Government of India, under Project Identification No. RTI 4006 (1303/3/2019/R&D-II/DAE/4749 dated 16.7.2020). AN and SC acknowledge a research fellowship from DBT.
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Tirumalai, V., Narjala, A., Swetha, C. et al. Cultivar-specific miRNA-mediated RNA silencing in grapes. Planta 256, 17 (2022). https://doi.org/10.1007/s00425-022-03934-y
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DOI: https://doi.org/10.1007/s00425-022-03934-y