Identifying MicroRNAs and Transcript Targets in Jatropha Seeds

Abstract

MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs.

Dynamics of miR156 and miR172 involved in the flowering of Jatropha curcas L.

“…In leaves, it had a peak expression in the vegetative stage and another at the time of floral transition, whereas in meristems it only had increased expression at the floral transition. Temporal tissue expression has already been described in J. curcas seeds, and each isomiRNA, for both miR172 and miR156, is expressed to different levels depending on the degree of their maturity (Galli et al 2014).…”

“…However, the aforementioned study did not report whether the target genes of these variants of miR156 are involved in the vegetative-reproductive transition of the plant (Galli et al 2014). Although a large number of miRNAs have been identified in various plants (Zeng et al 2010;Wang et al 2011;Vishwakarma & Jadeja 2013), only two studies have reported and validated the existence of miR156 and miR172 in J. curcas (Zeng et al 2010;Galli et al 2014).…”

The pivotal role of small non-coding RNAs in the regulation of seed development

“…Recent sRNA research related to oilseed content provides further examples of how specific miRNA-target interactions can be potentially used in breeding to improve seed nutritional value (Cao et al 2013;Zhao et al 2012;Wang et al 2016) or biodiesel production (Cao et al 2013;Galli et al 2014). Contrasting oilseed content genotypes appear to share a small percentage of unique sRNA sequences (Cao et al 2013), and available studies suggest some miRNAs are possibly associated with the different metabolic profiles presented by high-and low-oil-content seeds.…”

The Hevea brasiliensis AP2/ERF superfamily: from ethylene signalling to latex harvesting and physiological disease response

“…Furthermore, post-transcriptional regulation of AP2/ERF genes by microRNAs was also demonstrated. The JcDREB gene in Jatropha curcas has been targeted by miR156 (Galli et al, 2014) while a repression of expression of OitaAP2 gene in Orchis italica was controlled by miR172 (Salemme et al, 2013). In some cases, the action of miRs can be specific.…”