title: 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.
authors.affiliation: Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Arzuba
authors.initials: A
authors.lastname: Akter
authors.affiliation: Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Md Muzahidul
authors.initials: MM
authors.lastname: Islam
authors.affiliation: Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Shakhinur Islam
authors.initials: SI
authors.lastname: Mondal
authors.affiliation: Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Zabed
authors.initials: Z
authors.lastname: Mahmud
authors.affiliation: Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Nurnabi Azad
authors.initials: NA
authors.lastname: Jewel
authors.affiliation: Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Sabiha
authors.initials: S
authors.lastname: Ferdous
authors.affiliation: Computer Science and Engineering Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Md Ruhul
authors.initials: MR
authors.lastname: Amin
authors.affiliation: Food Engineering and Tea Technology Department, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
authors.forename: Md Mahfuzur
authors.initials: MM
authors.lastname: Rahman
keywords: Coffea arabica; Computational approach; Expressed sequence tags; MicroRNA