Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)

Abstract

MicroRNAs (miRNAs) are small (20-24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

WRKY1 acts as a key component improving resistance against Alternaria solani in wild tomato, Solanum arcanum Peralta

“…Co-expression networks were visualized with the Cytoscape program version 3.1.0 (Shannon et al, 2003). GO annotation of CEG was performed according to Barvkar et al (2013) with plant-specific database and expression value ≤e À20 (McCarthy et al, 2006).…”

Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development?

“…miR828 is the trigger for production of TAS4 siRNAs, and was originally thought to be unique to Arabidopsis , but has subsequently been found in grape [55], poplar ( Populus trichocarpa ) [56], cotton ( Gossypium hirsutum ) [57], cabbage ( Brassica rapa ) [58], flax ( Linum usitatissimum ) [59], soybean ( Glycine max ) [21], common bean ( Phaseolus vulgaris ) [60], clary sage ( Salvia sclarea ) [61], melon ( Cucumis melo ) [62], rose ( Rosa multiflora ) [63], tomato ( Solanum lycopersicum ) [64], tobacco ( Nicotiana tabacum and N. attenuata ) [65, 66], cocoa ( Theobroma cacao ) [67], Chinese apricot ( Prunus mume ) [68, 69], peach ( Prunus persica ) [70, 71], citrus ( Citrus sinensis ) [72], apple ( Malus domestica ) [73], hickory ( Carya cathayensis ) [74], cassava ( Manihot esculenta ) [75], Brazilian cherry ( Eugenia uniflora ) [76], Chinese tulip tree ( Liriodendron chinense ) [77], and Red Sea mangrove ( Avicennia marina ) [78]. Figure 1 shows a phylogram of the evolutionary relationships for eudicot species which have evidence of TAS4 in their genomes.…”

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

“…MiRNAs are 21-24 nt RNA sequences derived from the singlestranded RNA precursors, which possess the ability to form intra-molecular complementary hairpin structures. This feature distinguishes miRNAs from other sRNAs, such as small interfering RNAs, which originate from double-stranded RNAs derived from the inter-molecular hybridization of two complementary RNA molecules (Bej and Basak, 2014;Barvkar et al, 2013;Gursanscky et al, 2011). The application of miRNA as a novel type of genetic markers has been developed for genotyping applications in foxtail millet (Setaria italica L.) and related grass species (Yadav et al, 2014), in combination with the SSR markers in Oryza sativa (Mondal and Ganie, 2014) with the aim to identify the salt responsive miRNA-SSR markers and in the genotyping of Brassica species (Fu et al, 2013).…”