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

  • Tiffanie Y. Moss | tiffanie.moss@case.com Department of Biology, Case Western Reserve University, Cleveland, United States.
  • Christopher A. Cullis Department of Biology, Case Western Reserve University, Cleveland, United States.

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 Linum usitatissimum 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.

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Published
2012-06-05
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Articles
Keywords:
microRNA, bioinformatics, genome, flax, EST
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  • PDF: 472
  • Supplementary File 8. miRNA:target duplex structures for miRNA:5208.: 0
  • Supplementary File 9. miRNA:target duplex structures for pre-miRNA:932: 0
  • Supplementary File 7. miRNA:target duplex structures for Contig3977.: 0
  • Supplementary File 6. miRNA:target duplex structures for Contig6926: 0
  • Supplementary File 10. miRNA:target duplex structures for Scaffold1966 miRNAs: 0
  • Supplementary File 11. miRNA:target duplex structures for pre-miRNA:1209: 0
  • Supplementary File 14. The complete dataset for all miRNAs derived from the flax genome with predicted targets: 0
  • Legends for Supplementary Files: 0
  • Supplementary File 13: KEGG Pathway Analysis of Linum putative miRNA targets - breakdown by heirarchy subcategory: 0
  • Supplementary File 2. Flax UNIGENE derived miRNA hairpin structures.: 0
  • Supplimentary File 12: Targets of Flax miRNAs: 0
  • Supplementary File 1. Flax genome derived miRNA hairpin structures.: 0
  • Supplimentary File 5: Predicted targets for Unigene derived miRNAs.: 0
  • Supplementary File 4. Discarded flax UNGENE derived hairpin structures.: 0
  • Supplementary File 3. Discarded flax genome derived hairpin structures.: 0
How to Cite
Moss, T. Y., & Cullis, C. A. (2012). Computational prediction of candidate miRNAs and their targets from the completed Linum ussitatissimum genome and EST database. Journal of Nucleic Acids Investigation, 3(1), e2. https://doi.org/10.4081/jnai.2012.4150