Identification of microRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods

PLoS One. 2015 Mar 31;10(3):e0121542. doi: 10.1371/journal.pone.0121542. eCollection 2015.

Abstract

Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Brassicaceae / genetics*
  • Computational Biology*
  • High-Throughput Nucleotide Sequencing*
  • MicroRNAs / genetics*
  • RNA, Messenger / genetics*

Substances

  • MicroRNAs
  • RNA, Messenger

Associated data

  • SRA/SRS776891
  • SRA/SRS778709
  • SRA/SRS780909
  • SRA/SRS781487

Grants and funding

This work was supported by grants from the National Science Foundation (No. IOS-1339385), and the Department of Energy (DE-AR0000202) of the United States. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.