Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

Joann Diray-Arce,Brent L Nielsen,Bilquees Gul,Mark Clement,M Ajmal Khan

doi:10.1186/s12864-015-1553-x

Joann Diray-Arce, Brent L Nielsen + Show 3 more

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https://doi.org/10.1186/s12864-015-1553-x

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Abstract

BackgroundImprovement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of Suaeda fruticosa, a halophyte that has the ability to sequester salts in its leaves. Suaeda fruticosa is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores. This plant is an obligate halophyte that grows optimally from 200–400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. De novo assembly of the transcriptome and analysis has allowed identification of differentially expressed and unique genes present in this non-conventional crop.ResultsTwelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of Suaeda fruticosa. The transcriptome was assembled de novo using Velvet and Oases k-45 and clustered using CDHIT-EST. There are 54,526 unigenes; among these 475 genes are downregulated and 44 are upregulated when samples from plants grown under optimal salt are compared with those grown without salt. BLAST analysis identified the differentially expressed genes, which were categorized in gene ontology terms and their pathways.ConclusionsThis work has identified potential genes involved in salt tolerance in Suaeda fruticosa, and has provided an outline of tools to use for de novo transcriptome analysis. The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression and identification of genes that may be involved in salt tolerance. The transcriptome may serve as a reference sequence for study of other succulent halophytes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1553-x) contains supplementary material, which is available to authorized users.

Highlights

Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases
De novo transcriptome assembly and assessments of expressed sequenced tags Experimental design To prepare for the transcriptome assembly and analysis, total RNA was extracted from shoots and roots of Suaeda fruticosa
These include biological triplicates of cDNA libraries for S. fruticosa roots from plants grown without salt (R000), roots with 300 mM optimal salt (R300), shoots with no salt (S000) and shoots with 300 mM optimal salt (S300)

Summary

Introduction

Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. Suaeda fruticosa is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores This plant is an obligate halophyte that grows optimally from 200–400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. A succulent shrub in the family Chenopodiaceae, is an obligate halophyte that grows optimally at 300 mM NaCl and has the adaptation to reduce sodium buildup for long term survival [2] This perennial halophyte has a strong ability to accumulate and sequester Na+ and Cl− without the aid of salt glands, bladder or trichomes [3]. Similar to Suaeda fruticosa, the majority of halophytes do not have glands or external bladders to modulate their tissue ion concentration it has been seen to be a good model genus for the study of salt tolerance [12]

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