Computational identification of miRNA and targets from expressed sequence tags of coffee (Coffea arabica)

Abstract

MicroRNAs (miRNAs) are the group of ∼22 nucleotides long noncoding small endogenous and evolutionary conserved post-transcriptional regulatory RNAs, which show an enormous role in various biological and metabolic processes in both animals and plants. To date not a single miRNA has been identified in coffee (Coffea arabica), which is an economically important plant of Rubiaceae family. In this study a well-developed, powerful and comparative computational approach, EST-based homology search is applied to find potential miRNA of coffee. We blasted publicly available EST sequences obtained from NCBI GenBank against previously known plant miRNAs. For the first time, one potential miRNA from a large miRNA family with appropriate fold back structures was identified through a series of filtration criteria. A total of six potential target genes in Arabidopsis were identified based on their sequence complementarities. The target genes mainly encode transport inhibitor like protein, transcription factor, DNA-binding protein, and GRR1-like protein, and these genes play an important role in various biological processes like response to chitin, cold, salt stress, water deprivation etc. Overall, findings from this study will accelerate the way for further researches of miRNAs and their functions in coffee.

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

“…This indicates that miRNAs widely exist in the genus Coffea and further demonstrates that many miRNAs are highly evolutionary conserved among species in the plant kingdom. Similarly, only one miRNA was reported by Akter et al, (2014) in Coffea arabica, 58 miRNA sequences belonging to 33 miRNA families from Coffea canephora and Coffea arabica were reported by Loss-Morais et al (2014), and 18 miRNAs belonging to 14 miRNA families from Coffea arabica were reported by Rebijith et al, (2013). The miRNA families miR-160, -162, -164, -165, -171, -397, -408, -479, and -2111 were reported for only mature miRNA sequences by Loss-Morais et al (2014) and were also found in this study with pre-miRNA sequences and secondary self-folded stem-loop structures.…”

“…It also has medicinal properties because of secondary metabolites like polyphenols, caffeine, theobromine, and chlorogenic acids (Ferrazzano, 2009). To our knowledge, although progress has been made on the genus Coffea, there is little knowledge about miRNAs in Coffea (Rebijith et al, 2013;Akter et al, 2014;Loss-Morais et al, 2014). In this study, we employed a well-defined comparative genomebased homolog search to identify Coffea miRNAs.…”

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

“…Some in silico efforts have been performed to describe miRNAs in C. arabica [1,40], identifying 15 and 1 miRNA families, respectively. In addition to that, recently, deepsequencing libraries have been generated using both genomic [11] and transcriptomic [29] data of C. canephora.…”

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).…”