Identification of miRNA encoded byJatropha curcasfrom EST and GSS

Abstract

miRNAs are endogenous approx 22 nucleotide RNA which mediates transcriptional or Post-transcriptional gene regulation and play a critical role in diverse aspects of plant development. miRNA identification in wet lab have various constraints, it is time consuming and expensive. It also faces the limitation of identifying miRNAs expressed at specific time and/or at special conditions. Due to the nature of strong conservation of miRNA in plant species, the use of comparative genomics approach for expressed sequence tags (ESTs), Genome Survey Sequence (GSS) and structural feature criteria filter has paved the way toward the identification of conserved miRNAs from the plant species whose genomes are not yet available in public domain. To identify the novel miRNA from Jatropha curcas, a total of 46862 EST sequences and 1569 GSS were searched for homology to previously known viridiplantae 2502 mature miRNA. After predicting the RNA secondary structure, 24 new potential miRNA were identified in J. curcas. Using the newly identified miRNA sequences, a total of 78 potential target genes were identified for 3 miRNA families. Most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. These findings considerably broaden the scope of understanding the functions of miRNA in J. curcas.

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

“…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). This suggests the possibility that this pair of miRNAs is involved in the flowering of J. curcas.…”

Manipulating microRNAs for improved biomass and biofuels from plant feedstocks

“…Therefore, the least bioenergy‐relevant miRNAs among the highly conserved miRNA families are omitted entirely from the review (Figure ). Where there is a lack of experimentally validated miRNA data for biofuel feedstock species, we will speculate upon the relevant potential miRNA application to biofuel feedstocks based upon our knowledge of miRNA studies in Arabidopsis and other plant species (Vishwakarma and Jadeja, ; Xie et al ., ). Further research to experimentally validate target identification and miRNA–miRNA interaction in feedstock crops is necessary to corroborate such speculation.…”

Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus)

“…In addition, ESTs can be used as an alternative approach for the discovery of pre-miRNAs, particularly in species lacking a draft genome sequence. This approach has been used to identify many premiRNAs in various crops, including miRNAs from maize wheat (Han et al, 2009), sugarcane (Zanca et al, 2010), coffee (Akter et al, 2013); jatropha (Vishwakarma and Jadeja, 2013), and tomato (Din and Barozai, 2014).…”