Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses

Fengli Sun,Gaijuan Tang,Chao Zhang,Shudong Liu,Xi Peng,Yajun Xi

doi:10.1186/s12870-018-1288-3

Fengli Sun, Gaijuan Tang + Show 4 more

Open Access

https://doi.org/10.1186/s12870-018-1288-3

Copy DOI

Abstract

BackgroundLong non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. Studies of lncRNAs in non-model plants are quite limited, especially those investigating multiple dehydration stresses. In this study, we identified novel lncRNAs and analyzed their functions in dehydration stress memory in switchgrass, an excellent biofuel feedstock and soil-conserving plant in the Gramineae family.ResultsWe analyzed genome-wide transcriptional profiles of leaves of 5-week-old switchgrass plantlets grown via tissue culture after primary and secondary dehydration stresses (D1 and D2) and identified 16,551 novel lncRNAs, including 4554 annotated lncRNAs (targeting 3574 genes), and 11,997 unknown lncRNAs. Gene ontology and pathway enrichment analysis of annotated genes showed that the differentially expressed lncRNAs were related to abscisic acid (ABA) and ethylene (ETH) biosynthesis and signal transduction, and to starch and sucrose metabolism. The upregulated lncRNAs and genes were related to ABA synthesis and its signal transduction, and to trehalose synthesis. Meanwhile, lncRNAs and genes related to ETH biosynthesis and signal transduction were suppressed. LncRNAs and genes involved in ABA metabolism were verified using quantitative real-time PCR, and the endogenous ABA content was determined via high performance liquid chromatography mass spectrometry (HPLC-MS). These results showed that ABA accumulated significantly during dehydration stress, especially in D2. Furthermore, we identified 307 dehydration stress memory lncRNAs, and the ratios of different memory types in switchgrass were similar to those in Arabidopsis and maize.ConclusionsThe molecular responses of switchgrass lncRNAs to multiple dehydration stresses were researched systematically, revealing novel information about their transcriptional regulatory behavior. This study provides new insights into the response mechanism to dehydration stress in plants. The lncRNAs and pathways identified in this study provide valuable information for genetic modification of switchgrass and other crops.

Highlights

IntroductionLong non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses
Long non-coding RNAs play important roles in plant growth and stress responses
1597 differentially expressed Long non-coding RNA (lncRNA) were identified under repeated dehydration stresses (Additional file 2: Table S4), and they were distributed across all chromosomes, similar to the distribution of total lncRNAs (Fig. 2b, c)

Summary

Introduction

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. Plants suffer thousands of dehydration stresses throughout their lifecycle, and may even experience multiple stresses over a few days. In Arabidopsis, 2708 expressed lincRNAs [20] and 20 Fusarium oxysporumresponsive lncTARs (long non-coding transcriptionally active regions) were identified [18], with 245 poly(A) + and 58 poly(A)– lncRNAs differentially expressed under various stress stimuli (drought, salinity, cold, and heat) [17]. Aside from Arabidopsis [33] and rice, stress-responsive lncRNAs have been identified in cotton [25], maize [21], wheat [22], and Medicago truncatula [31]

Methods

Results

Discussion

Conclusion