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.