De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

Elham Younesi-Melerdi,Mohammad Reza Bakhtiarizadeh,Ghorban-Ali Nematzadeh,Ali Pakdin-Parizi,Seyed Abolfazl Motahari

doi:10.1038/s41598-020-65947-5

Abstract

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log2FC > 1 and FDR < 0.01) showed that 1861 transcripts expressed differentially, including169 up and 316 down-regulated transcripts in 200 mM NaCl treatment and 1035 up and 430 down-regulated transcripts in 400 mM NaCl treatment compared to control. In addition, 89 transcripts were common in both treatments. The most important over-represented terms in the GO analysis of differentially expressed genes (FDR < 0.05) were chitin response, response to abscisic acid, and regulation of jasmonic acid mediated signaling pathway under 400 mM NaCl treatment and cell cycle, cell division, and mitotic cell cycle process under 200 mM treatment. In addition, the phosphatidylcholine biosynthetic process term was common in both salt treatments. Interestingly, under 400 mM salt treatment, the PRC1 complex that contributes to chromatin remodeling was also enriched along with vacuole as a general salinity stress responsive cell component. Among enriched pathways, the MAPK signaling pathway (ko04016) and phytohormone signal transduction (ko04075) were significantly enriched in 400 mM NaCl treatment, whereas DNA replication (ko03032) was the only pathway that significantly enriched in 200 mM NaCl treatment. Finally, our findings indicate the salt-concentration depended responses of A. littoralis, which well-known salinity stress-related pathways are induced in 400 mM NaCl, while less considered pathways, e.g. cell cycle and DNA replication, are highlighted under 200 mM NaCl treatment.

Highlights

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs
The results showed that the differentially expressed genes (DEGs) selected for validation exhibited similar up or down-regulation patterns as those shown from RNA sequencing (RNA-seq) data analysis (Fig. 6), the observed relative expression differences between RNA-seq and qRT-PCR is owing to intrinsic features of these methods
In this study the A. littoralis responses to salinity stress at transcriptome level were investigated by de novo RNA-seq analysis

Summary

Introduction

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. Halophyte plants are adapted for living in extreme environments and constitute about 1% of the Earth’s flora[3] These plants are ideal candidates for studying and exploring the complex physiological and molecular mechanisms of salt resistance[11]. The transcriptome analysis of A. littoralis in different salt stress conditions can extend the molecular knowledge and identifying undercover mechanisms of salt resistance in halophytes. These findings can be subsequently used for improving economically important crop plants in genetic engineering and plant breeding programs. This study is the first report of high-throughput analysis (de novo RNA-Seq) of A. littoralis transcriptome that provides new insights at molecular responses of halophytes to salinity

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