J Integr Plant Biol. ›› 2018, Vol. 60 ›› Issue (11): 1070-1082.DOI: 10.1111/jipb.12693

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Genome-wide screening of long non-coding RNAs involved in rubber biosynthesis in Eucommia ulmoides

Huimin Liu1, Yan Lu2, Juan Wang3, Jingjing Hu4 and Tana Wuyun1*   

  1. 1State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China
    2State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
    3Chemistry department, University of Missouri-Columbia, Columbia MO 65201, USA
    4Inertia Shanghai Biotechnology Co., Ltd., Shanghai 200335, China

    *Correspondence:

    Email: Tana Wuyun (tanatanan@163.com)
  • Received:2018-03-02 Accepted:2018-06-25 Online:2018-07-03 Published:2018-11-01

Abstract:

Increasing evidence indicates that long non-coding RNAs (lncRNAs) play pivotal roles in regulatory networks controlling plant and animal gene expression. However, lncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber (Eu-rubber), are currently unknown. Here, we report on RNA deep-sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,103 lncRNAs and 9,048 transcripts of uncertain coding potential (TUCPs) were identified. Two differentially expressed (DE) TUCPs appear to simultaneously regulate 12 protein-coding genes involved in Eu-rubber biosynthesis (GIEBs), as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu-rubber is synthesized. A model is proposed in which “commanders” (DE TUCPs) direct the “builders” (DE genes) to construct a “storehouse” of materials needed for Eu-rubber synthesis, and the “workers” (GIEBs) to synthesize Eu-rubber. These findings provide insights into both cis- and trans-polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.

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