Computational prediction of candidate miRNAs and their targets from the completed Linum ussitatissimum genome and EST database

Abstract

Flax is an important agronomic crop grown for its fiber (linen) and oil (linseed oil). In spite of many thousands of years of breeding some fiber varieties have been shown to rapidly respond to environmental stress with heritable changes to its genome. Many miRNAs appear to be induced by abiotic or biotic conditions experienced through the plant life cycle. Computational miRNA analysis of the flax genome provides a foundation for subsequent research on miRNA function in <em>Linum usitatissimum </em>and may also provide novel insight into any regulatory role the RNAi pathway may play in generating adaptive structural variation in response to environmental stress. Here a bioinformatics approach is used to screen for miRNAs previously identified in other plant species, as well as to predict putative miRNAs unique to a particular species which may not have been identified as they are less abundant or dependent upon a specific set of environmental conditions. Twelve miRNA genes were identified in flax on the basis of unique pre-miRNA positions with structural homology to plant pre-miRNAs and complete sequence homology to published plant miRNAs. These miRNAs were found to belong to 7 miRNA families, with an additional 2 matches corresponding to as yet unnamed poplar miRNAs and a parologous miRNA with partial sequence homology to mtr-miR4414b. An additional 649 novel and distinct flax miRNA genes were identified to form from canonical hairpin structures and to have putative targets among the ~30,000 flax Unigenes.

miR319, miR390, and miR393 Are Involved in Aluminum Response in Flax (Linum usitatissimum L.)

“…In previous flax studies, potential targets for some miRNAs from miR319, miR390, and miR393 families were predicted [ 21 , 38 , 39 ]. Here, we performed target prediction for flax highly-expressed miRNAs from miR319, miR390, and miR393 families (Supplementary Table 3).…”

Stress-Induced Genetic Change in Flax Reveals Genome Variation Mechanism

“…If some sequences are newly formed, they have to be copied from a brand new nucleotide sequence so small non-coding RNA may be responsible for this due to their mimic character by which the new sequence was made and copied to the original DNA. This may also explain the potential miRNA sequences encoded by LIS-1(Moss and Cullis, 2012). If this is right, maybe RNA is the involved in facilitating the genomic change.…”