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Authors Diray-Arce, J; Clement, M; Gul, B; Khan, MA; Nielsen, BL
Author Full Name Diray-Arce, Joann; Clement, Mark; Gul, Bilquees; Khan, M. Ajmal; Nielsen, Brent L.
Title Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance
Source BMC GENOMICS
Language English
Document Type Article
Author Keywords Halophytes; Suaeda; RNA-seq; Differential expression; Transcriptome profiling; De novo assembly; Transcriptome; Salt tolerance
Keywords Plus PROTEIN PHOSPHATASE CALCINEURIN; FALSE DISCOVERY RATE; CADMIUM ACCUMULATION; SALINITY STRESS; DELLA PROTEINS; ARABIDOPSIS; GENOME; RICE; GROWTH; RESPONSES
Abstract Background: 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. 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. Results: Twelve 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. Conclusions: This 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.
Author Address [Diray-Arce, Joann; Nielsen, Brent L.] Brigham Young Univ, Dept Microbiol & Mol Biol, Provo, UT 84602 USA; [Clement, Mark] Brigham Young Univ, Dept Comp Sci, Provo, UT 84602 USA; [Gul, Bilquees] Univ Karachi, Inst Sustainable Halophyte Utilizat, Karachi, Pakistan; [Khan, M. Ajmal] Qatar Univ, Coll Arts & Sci, Doha, Qatar
Reprint Address Nielsen, BL (corresponding author), Brigham Young Univ, Dept Microbiol & Mol Biol, Provo, UT 84602 USA.
E-mail Address brentnielsen@byu.edu
ResearcherID Number Khan, M. Ajmal/L-7721-2015
ORCID Number Khan, M. Ajmal/0000-0003-2837-0794; Arce, Joann Diray/0000-0003-2183-4269
Funding Agency and Grant Number Pakistan-U.S. Science and Technology Cooperation Program; Department of Microbiology and Molecular Biology at Brigham Young University; U.S. Dept. of State and Higher Education Commission of Pakistan
Funding Text Special thanks to Justin Page and Dr. Joshua Udall for guiding transcriptome analysis and experimental design and for Nielsen Lab members Collin Hansen, Daniel Ricks and Kevin Prier for helping with the wet lab preparations. This research has been supported by a grant from the Pakistan-U.S. Science and Technology Cooperation Program, U.S. Dept. of State and Higher Education Commission of Pakistan, and by the Department of Microbiology and Molecular Biology at Brigham Young University.
Times Cited 35
Total Times Cited Count (WoS, BCI, and CSCD) 36
Publisher BMC
Publisher City LONDON
Publisher Address CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
ISSN 1471-2164
29-Character Source Abbreviation BMC GENOMICS
ISO Source Abbreviation BMC Genomics
Publication Date MAY 6
Year Published 2015
Volume 16
Article Number 353
Digital Object Identifier (DOI) 10.1186/s12864-015-1553-x
Page Count 24
Web of Science Category Biotechnology & Applied Microbiology; Genetics & Heredity
Subject Category Biotechnology & Applied Microbiology; Genetics & Heredity
Document Delivery Number CH3OA
Unique Article Identifier WOS:000353938800005
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