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Comprehensive Analysis of Differentially Expressed Unigenes under NaCl Stress in Flax (Linum usitatissimum L.) Using RNA-Seq
- Source :
- International Journal of Molecular Sciences, Volume 20, Issue 2, International Journal of Molecular Sciences, Vol 20, Iss 2, p 369 (2019)
- Publication Year :
- 2019
- Publisher :
- MDPI AG, 2019.
-
Abstract
- Flax (Linum usitatissimum L.) is an important industrial crop that is often cultivated on marginal lands, where salt stress negatively affects yield and quality. High-throughput RNA sequencing (RNA-seq) using the powerful Illumina platform was employed for transcript analysis and gene discovery to reveal flax response mechanisms to salt stress. After cDNA libraries were constructed from flax exposed to water (negative control) or salt (100 mM NaCl) for 12 h, 24 h or 48 h, transcription expression profiles and cDNA sequences representing expressed mRNA were obtained. A total of 431,808,502 clean reads were assembled to form 75,961 unigenes. After ruling out short-length and low-quality sequences, 33,774 differentially expressed unigenes (DEUs) were identified between salt-stressed and unstressed control (C) flax. Of these DEUs, 3669, 8882 and 21,223 unigenes were obtained from flax exposed to salt for 12 h (N1), 24 h (N2) and 48 h (N4), respectively. Gene function classification and pathway assignments of 2842 DEUs were obtained by comparing unigene sequences to information within public data repositories. qRT-PCR of selected DEUs was used to validate flax cDNA libraries generated for various durations of salt exposure. Based on transcriptome sequences, 1777 EST-SSRs were identified of which trinucleotide and dinucleotide repeat microsatellite motifs were most abundant. The flax DEUs and EST-SSRs identified here will serve as a powerful resource to better understand flax response mechanisms to salt exposure for development of more salt-tolerant varieties of flax.
- Subjects :
- 0106 biological sciences
0301 basic medicine
UniGene
RNA-Seq
Sodium Chloride
01 natural sciences
lcsh:Chemistry
Transcriptome
Gene Expression Regulation, Plant
Transcription (biology)
Cluster Analysis
lcsh:QH301-705.5
Spectroscopy
Expressed Sequence Tags
Genetics
High-Throughput Nucleotide Sequencing
General Medicine
Up-Regulation
Computer Science Applications
Linum
flax
Down-Regulation
Biology
Genes, Plant
Article
Catalysis
Inorganic Chemistry
03 medical and health sciences
Stress, Physiological
EST-SSR
Complementary DNA
Physical and Theoretical Chemistry
Molecular Biology
Gene
Sequence Analysis, RNA
cDNA library
Gene Expression Profiling
Organic Chemistry
Reproducibility of Results
Molecular Sequence Annotation
biology.organism_classification
NaCl stress
030104 developmental biology
lcsh:Biology (General)
lcsh:QD1-999
DEUs
RNA-seq
Microsatellite Repeats
010606 plant biology & botany
Subjects
Details
- ISSN :
- 14220067
- Volume :
- 20
- Database :
- OpenAIRE
- Journal :
- International Journal of Molecular Sciences
- Accession number :
- edsair.doi.dedup.....f0fe33a5c9c484f71c38d807341770ee
- Full Text :
- https://doi.org/10.3390/ijms20020369