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

Abstract

IntroductionMicroRNAs (miRNAs) are an extensive class of noncoding small endogenous RNAs of 18 to 26 nt in length that are derived from self-complementary fold-back structures of longer precursor sequences (pre-miRNAs) and are generated by Dicer-like 1 (DCL1) in plants (Bartel, 2004). Mature miRNAs inhibit gene expression at posttranscriptional levels by either targeting mRNAs for degradation or inhibiting protein translation. Both processes are accomplished by the complementary base pairing of miRNAs to their target mRNA sequences (Ambros, 2004). In plants, for a majority of cases, miRNAs interact with their targets through perfect or near-perfect base pairing and lead to target mRNA degradation (Jones-Rhoades et al., 2006). Increasing evidence has revealed that miRNAs play an important role in a wide range of development processes in plants, including cell proliferation, stress response, metabolism, inflammation, and signal transduction (Ambros, 2004;Jones-Rhoades et al., 2006;Zhang et al., 2007a;Ali et al., 2016) and crosskingdom gene regulation (Barozai and Din, 2017). To date, more than 28,645 miRNAs have been identified from 223 species of plants and animals and deposited in the publicly available database miRBase (Release 21) (Griffiths-Jones et al., 2008). The majority of plant miRNAs have been found in species with fully sequenced genomes including 713 from Oryza sativa, 401 from Populus trichocarpa, 384 from Arabidopsis thaliana, 343 from Solanum tuberosum, 321 from Zea mays, and 241 from Sorghum bicolor (Griffiths-Jones et al., 2008). miRNA-related research is continuously growing and miRNAs, along with their functions, are being identified and elucidated using a wide variety of computational tools and experimental methods including direct cloning, deep sequencing, and other approaches. Comparison of miRNAs across multiple plant species has demonstrated that some miRNAs are highly evolutionary conserved from species to species, such as from mosses to higher flowering eudicots in the plant kingdom (Floyd and Bowman, 2004;Zhang et al., 2006aZhang et al., , 2006b. Conservation of miRNA sequences has provided a powerful strategy for identifying miRNAs in other species. Currently, comparative genome-based homolog searches have been used to identify conserved miRNAs in many plant species, including cotton (

Bioinformatics prediction and annotation of cherry ( Prunus avium L.) microRNAs and their targeted proteins

“…Similar ranges of MFE, number of mismatches, mature miRNA length, pre-miRNA length, Watson-Crick or G/U pairing, and 3'/5' residency have been reported in various plants by different researchers in Phaseolus (Barozai et al, 2013), tomato (Din and Barozai, 2014a), eggplant (Din and Barozai, 2014b), coffee (Bibi et al, 2017), switchgrass (Barozai et al, 2018a), and Porphyridium cruentum (Barozai et al, 2018b). The agreement of results with previous reports reinforces the validation of the cherry miRNAs.…”

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

“…Comparing our results with previously identified C. canephora miRNAs [18][19][20][21][22][23][24], we identified seven new precursors and 18 new mature miRNAs for C. canephora (Tables S12 and S13, Supplementary File S2, Supplementary File S3).…”

“…A total of seven studies have predicted miRNAs in C. canephora using distinct approaches. Five studies have focused only on prediction [18][19][20][21][22]. Two studies have used small RNA sequencing to confirm the transcriptional activity of miRNAs [23,24].…”

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

“…A good percentage of GC content (> 40%) in the miRNA sequences further specified their stability [40]. When examined terpene biosynthesis, the miRNA families, miR2108, miR4993, miR396, miR5015, and miR414, targeting terpene pathway genes were more or less in agreement with the previous findings on terpene biosynthesis occurring in different plant species, Mentha spp., Z. officinale [30], Coffea [76], W. somnifera [41] and Viscum album L. [77]. As far as tartaric acid biosynthesis is concerned, this study, for the first time, detected miRNAs, belonging to 11 miR families, which could be associated with the post-transcriptional or translational regulation of this pathway.…”

“…However, miRNAs of a family may not be conserved with respect to their sequence and/or secondary structure . Significantly negative MFE and MEFI value stipulated appropriate folding and stable secondary structures of the predicted miRNAs . A good percentage of GC content (> 40%) in the miRNA sequences further specified their stability .…”