High-Throughput Sequencing and Degradome Analysis Identify miRNAs and Their Targets Involved in Fruit Senescence of Fragaria ananassa

Abstract

In non-climacteric fruits, the respiratory increase is absent and no phytohormone is appearing to be critical for their ripening process. They must remain on the parent plant to enable full ripening and be picked at or near the fully ripe stage to obtain the best eating quality. However, huge losses often occur for their quick post-harvest senescence. To understanding the complex mechanism of non-climacteric fruits post-harvest senescence, we constructed two small RNA libraries and one degradome from strawberry fruit stored at 20°C for 0 and 24 h. A total of 88 known and 1224 new candidatemiRNAs, and 103 targets cleaved by 19 known miRNAs families and 55 new candidatemiRNAs were obtained. These targets were associated with development, metabolism, defense response, signaling transduction and transcriptional regulation. Among them, 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence. The present study provided valuable information for understanding the quick senescence of strawberry fruit, and offered a foundation for studying the miRNA-mediated senescence of non-climacteric fruits.

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

“…3 ananassa is a hybrid octoploid and poses tremendous challenges in genetic and genomic studies. Past studies of cultivated strawberry, including miRNA identification (Ge et al, 2013;Li et al, 2013;Xu et al, 2013), were mostly focused on the ripening stage fruit. In this work, we focused our analysis on F. vesca, a diploid wild strawberry whose genome has been sequenced (Shulaev et al, 2011).…”

MicroRNAs play an important role in the regulation of strawberry fruit senescence in low temperature

“…Moreover, by mapping all unique sRNA sequences to the strawberry genome and predicting the secondary structures of the candidate miRNA precursors, 1224 unique novel mature potential candidate miRNAs corresponding to 1157 pre-miRNAs were identified, of which most were 24 nt in length (Appendix B). These data were the same with previous work of Xu et al (2013), which have been submitted to the Gene Expression Omnibus under the accession number GSE48055.…”

“…The sRNA library construction, sequencing and data analysis were performed according to the methods of Xu et al (2013).…”

“…org/) were identified, but function of most miRNA is still unknown. To totally understand their biological functions in diverse biological processes, the recent development of degradome sequencing provided a new strategy for validating the splicing targets on a whole genome scale, which revolutionized the traditional computational target prediction and was successfully employed on identifying miRNA targets in plants ( Addo-Quaye et al, 2008;Xu et al, 2012Xu et al, , 2013.…”

“…In the previous work, to investigate the mechanism of postharvest senescence of strawberry fruit at ambient temperature (20 C), two sRNA libraries (fruit stored at 20 C for 0 and 24 h) and one degradome library (mixture of strawberries stored for 0 and 24 h) from strawberry fruit that were constructed and sequenced on an Illumina Hiseq 2500, and many miRNAs involved in fruit senescence were obtained (Xu et al, 2013). Here, in order to further understand the role of miRNAs on delaying senescence of strawberry fruit in response to low temperature (4 C), two other sRNA libraries (fruit stored at 4 C for 24 and 48 h, respectively) from strawberry fruit that were constructed and sequenced.…”