Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq

Abstract

Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus.

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

“…Transcript expression analysis revealed a Pearson Correlation Coefficient of 0.62 ( P < 0.05), providing evidence for a strong correlation between NERDL and its putative target gene, PtoNERD ( Figure 1C ). LncRNAs are usually shorter and are expressed at lower levels than protein-coding transcripts in P. tomentosa (Chen et al, 2015) and in mammals (Pauli et al, 2012). Here, RT-qPCR analysis and RNA-seq showed that the expression level of PtoNERD was higher than that of NERDL and that they both exhibit tissue-specific expression in P. tomentosa ( Figure 1C and Supplementary Figure S3 ).…”

Battles and hijacks: noncoding transcription in plants

“…Furthermore, 51 lincRNAs were identified as putative targets, and another 20 as target mimics, of known Populus miRNAs [20]. In Populus tomentosa, over 1300 putative lncRNAs were identified by RNA-seq, of which 776 were enriched in different wood tissues [21]. The maize (Zea mays) full-length cDNA sequencing project [22] yielded over 1900 noncoding genes [23].…”

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

“…Plant lncRNAs are expected to play important roles in plant development and the response to environment conditions, and thousands of lncRNAs have been identified in plants (Liu et al, 2012;Li et al, 2014;Shuai et al, 2014;Wang et al, 2014;Zhang et al, 2014b;Chen et al, 2015). However, revealing the functions of plant Figure 7.…”