Abstract
Salinity and drought stress are the primary cause of crop losses worldwide. In sodic saline soils sodium chloride (NaCl) disrupts normal plant growth and development. The complex interactions of plant systems with abiotic stress have made RNA sequencing a more holistic and appealing approach to study transcriptome level responses in a single cell and/or tissue. In this work, we determined the Petunia transcriptome response to NaCl stress by sequencing leaf samples and assembling 196 million Illumina reads with Trinity software. Using our reference transcriptome we identified more than 7,000 genes that were differentially expressed within 24 h of acute NaCl stress. The proposed transcriptome can also be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome and it is available at the SOL Genomics Network (SGN) http://solgenomics.net. Genes related to regulation of reactive oxygen species, transport, and signal transductions as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. The candidate genes identified in this study can be applied as markers for breeding or to genetically engineer plants to enhance salt tolerance. Gene Ontology analyses indicated that most of the NaCl damage happened at 24 h inducing genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions. Finally, we report a modification to the library preparation protocol whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the RNA-seq data. The methodological improvement presented here could substantially reduce the cost of sample preparation for future high-throughput RNA sequencing experiments.
Highlights
Abiotic stress is the negative effect on living organisms of nonliving factors such as high temperature, drought and salinity
In this work we present the most in-depth Petunia hybrida reference transcriptome by paired-end sequencing cDNA libraries
We evaluated if library construction with these two types of oligonucleotides resulted in significant differences by separately analyzing and comparing the output of both datasets (NH vs. HPLC purified primers (HP)) using different bioinformatics statistical analyses
Summary
Abiotic stress is the negative effect on living organisms of nonliving factors such as high temperature, drought and salinity. Abiotic stress affects normal plant growth and development and severely reduces agricultural productivity. Especially salinity and drought, are the primary cause of crop loss worldwide, leading to 50% average yield reductions per year for major crops [1,2]. Root proteomic profiling in four tomato (Solanum lycopersicum) accessions (Roma, Super Marmande, Cervil and Levovil) was conducted in response to short-term stress by exposing hydroponically grown plants to 100 mM NaCl [3], and a cDNA microarray was used on two cultivated tomato genotypes (LA2711 and ZS-5) growing hydroponically under 150 mM NaCl to study gene expression in early stages of development in tomato plants [4].
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