Show simple item record

AuthorDiray-Arce, Joann
AuthorClement, Mark
AuthorGul, Bilquees
AuthorKhan, M. Ajmal
AuthorNielsen, Brent L.
Available date2016-11-15T07:58:41Z
Publication Date2015-05-06
Publication NameBMC Genomics
Identifierhttp://dx.doi.org/10.1186/s12864-015-1553-x
CitationDiray-Arce J, Clement M, Gul B, Khan MA, Nielsen BL. Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics. 2015;16(1):353.
ISSN1471-2164
URIhttp://hdl.handle.net/10576/5003
AbstractBackground 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.
SponsorPakistan-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.
Languageen
PublisherBioMed Central
SubjectHalophytes
Salt tolerance
Transcriptome
De novo assembly
Transcriptome profiling
Differential expression
RNA-seq
Suaeda
TitleTranscriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance
TypeArticle
Volume Number16


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record