Identification of Ethylene Responsive miRNAs and Their Targets from Newly Harvested Banana Fruits Using High-Throughput Sequencing

Abstract

The roles of microRNAs (miRNAs) related to ethylene response in banana fruits remain unknown because many miRNAs are differentially expressed as the fruit ripens, making the identification of ethylene-responsive miRNAs difficult. Using newly harvested banana fruits (within 5 h after harvest) as material, we found that these fruit did not ripen when treated with 5 μL/L of ethylene for 12 h at 22 °C. Two miRNA libraries were generated from newly harvested banana fruits with and without ethylene treatment and sequenced. In total, 128 known miRNAs belonging to 42 miRNA families were obtained, and 12 novel miRNAs were identified. Among them, 22 were differentially expressed in response to ethylene treatment, among which 6 known miRNAs and their putative targets were validated using qRT-PCR. These putative targets encoded proteins including GATA, ARF, DLC, and AGO, etc. KEGG and GO analyses showed that miRNAs differentially expressed in response to ethylene mainly function in the molecular and biological processes.

Integration of Transcriptomes, Small RNAs, and Degradome Sequencing to Identify Putative miRNAs and Their Targets Related to Eu-Rubber Biosynthesis in Eucommia ulmoides

“…As with other plants, the majority of conserved miRNAs also had high abundance in E. ulmoides . Additionally, miR159, miR166 and miR396 had high expression levels in the majority of plants [5,42,44]. As expected, eu-miR159 was the most abundant in E. ulmoides , followed by eu-miR166a-3p, and eu-miR396 had moderate prevalence.…”

“…Previous studies had shown that most conserved miRNAs were more abundantly expressed in various tissues and developmental stages of plants, whereas the abundance of non-conserved miRNAs was relatively low [42,43]. As with other plants, the majority of conserved miRNAs also had high abundance in E. ulmoides .…”

Small RNAs, Degradome, and Transcriptome Sequencing Provide Insights into Papaya Fruit Ripening Regulated by 1-MCP

“…In banana, 12 novel and 128 known miRNAs were identified. Among these miRNAs, 22 were differentially expressed after ethylene regulation treatment and were involved in the ethylene response [ 30 ]. In Wang’s (2020) study between wild-type and LeERF1 transgenic tomato fruits, 9 miRNAs and 12 nat-siRNAs were found to be differentially expressed [ 40 ].…”

“…This showed that they were under the regulation of early auxin-responsive gene expression in the auxin signaling pathway [ 29 ]. An analysis of the differential expression of miRNAs in banana under ethylene treatment found that miR162a , miR167a , miR172a , and miR319a participated in ethylene-dependent fruit ripening [ 30 ]. All these results suggested that miRNAs play critical roles in plant development and fruit ripening by regulating ethylene targets, auxin, and other signaling pathways.…”

Emerging Connections between Small RNAs and Phytohormones

“…Two downstream TFs, EIN3 and EIN3-LIKE1 (EIL1) further induce numerous ETHYLENE RESPONSIVE FACTORs (ERFs) [5], which promote stress-responsive genes. Although the roles of ABA and ethylene in abiotic stress response are extensively studied, sheding light on the ABA/Et-controlled gene expression changes, it is unclear how and why ABA/Et also alter the levels of sRNAs in multiple species [99][100][101][102][103][104][105][106][107]. Excitingly, overexpression of some of these ABA-responsive sRNAs, like ath-miR168/393/394, renders arabidopsis more resistant to drought or salinity, suggesting that miRNAs are involved in the ABA-mediated drought response [108][109][110].…”