The small RNA repertoire in phloem tissue of three Vitis vinifera cultivars

The economic importance of the grapevine industry creates the need for the generation of genomic resources to ensure the sustainability of the industry. These resources will extend the knowledge of grapevine physiology, cultivar-specific characteristics and understanding how diseases and environmental conditions affect the plant. Small non-coding RNAs (sRNAs) are regulator molecules that can influence normal development and/or responses to environmental stimuli. In this study, next-generation sequencing (NGS) and bioinformatic analyses were used to identify sRNA species in grapevine phloem tissue. Forty-five novel mature Vitis vinifera miRNAs were identified and the presence of ten was validated using stemloop RT-qPCRs. Both non-coding and protein-coding gene regions were identified as putative phased loci of which the majority of the protein-coding gene loci were identified as disease resistance proteins. Potential phase-initiating miRNAs were also identified. A high number of sRNAs originating from repeat sequences were identified in all cultivar groups. This study also confirmed the non-random manner in which tRNA-derived sRNAs originate. The number of tRNA halves identified in Chenin blanc was lower compared to the other cultivar groups investigated. The identification of these different sRNAs extends the grapevine sRNA knowledge base significantly and can contribute to the unravelling of sRNA regulation in plants, potentially creating tools for grapevine functional studies.