De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance

Soumya Shree Nayak,Seema Pradhan,Dinabandhu Sahoo,Ajay Parida

doi:10.1038/s41598-020-61857-8

Abstract

With the rapidly deteriorating environmental conditions, the development of stress tolerant plants has become a priority for sustaining agricultural productivity. Therefore, studying the process of stress tolerance in naturally tolerant species hold significant promise. Phragmites karka is an invasive plant species found abundantly in tropical and sub tropical regions, fresh water regions and brackish marshy areas, such as river banks and lake shores. The plant possesses the ability to adapt and survive under conditions of high salinity. We subjected P. karka seedlings to salt stress and carried out whole transcriptome profiling of leaf and root tissues. Assessing the global transcriptome changes under salt stress resulted in the identification of several genes that are differentially regulated under stress conditions in root and leaf tissue. A total of 161,403 unigenes were assembled and used as a reference for digital gene expression analysis. A number of key metabolic pathways were found to be over-represented. Digital gene expression analysis was validated using qRT-PCR. In addition, a number of different transcription factor families including WRKY, MYB, CCCH, NAC etc. were differentially expressed under salinity stress. Our data will facilitate further characterisation of genes involved in salinity stress tolerance in P. karka. The DEGs from our results are potential candidates for understanding and engineering abiotic stress tolerance in plants.

Highlights

With the rapidly deteriorating environmental conditions, the development of stress tolerant plants has become a priority for sustaining agricultural productivity
In order to analyse the effect of salinity stress at the molecular level, eight-paired end libraries were generated for leaf and root tissue samples of Phragmites karka in replicates
De novo assembly of the reads using BinPacker[21] and rnaSPAdes[22] assemblers generated a total of 161,403 unigenes. Both software packages have been developed to be more flexible in their assembly parameters and thereby provide a more comprehensive transcriptome assembly compared to others[23]

Summary

Introduction

With the rapidly deteriorating environmental conditions, the development of stress tolerant plants has become a priority for sustaining agricultural productivity. One of the reasons for invasiveness of P. karka is its ability to tolerate higher levels of salinity than associated species, which inhibits the growth and development of other plants by hindering various metabolic activities, cell expansion and by triggering programmed cell death[9]. It is hypothesized that genetic and genomic analysis of halophytes, such as P. karka may lead to identification of novel metabolic pathways, mechanisms and genes involved in modulating salinity stress tolerance in crop plants[12]. The pathways and genes that are involved in salt tolerance have been reported in model plants like Arabidopsis and rice[13].The present communication reports a comprehensive RNASeq-based transcriptomic analysis of tissue samples (root and leaf) of P. karka exposed to different salinity treatments, and the validation of digital expression analysis by qRT PCR. This study reports identification of SSRs in the P. karka transcriptome

Methods

Results

Conclusion