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De novo transcriptome sequencing and identification of genes related to salt stress in Eucommia ulmoides Oliver

Wang, Lin, Du, Hongyan, Li, Tiezhu, Wuyun, Ta-na
Trees 2018 v.32 no.1 pp. 151-163
DNA libraries, Eucommia ulmoides, microsatellite repeats, osmoregulation, quantitative polymerase chain reaction, reactive oxygen species, salt stress, sequence analysis, signal transduction, sodium chloride, stress response, transcription factors, transcriptome, transcriptomics, unigenes
KEY MESSAGE: We used RNA sequencing to identify differentially expressed genes that improve our understanding of the salt stress response in Eucommia ulmoides. The native Chinese species Eucommia ulmoides is an economically important plant that grows in a wide range of conditions, including under salt stress. However, little is known about the genes and underlying molecular mechanisms involved in their salt stress response. The objective of this study was to investigate changes in the E. ulmoides transcriptome under salt stress. Four sequencing libraries were obtained from the control and salt stress (150 mM NaCl for 24 h) groups using Illumina HiSeq 2000. Approximately 181,071,150 clean reads were assembled de novo into 107,207 unigenes with an N50 length of 1032 bp. Among 437 differentially expressed genes (DEGs) between the control and salt stress group, 214 DEGs were upregulated and 223 DEGs were downregulated. Quantitative real-time PCR showed that DEG expression profiles were consistent with those from RNA sequencing. Functional annotation analysis indicated that many DEGs could be involved in signal transduction, ion transport, osmotic regulation and reactive oxygen species scavenging. Furthermore, 79 transcription factor families in 1590 unigenes and 32,646 simple sequence repeats (SSR) in 24,582 unigenes were identified. Overall, this study provided new insights into the molecular mechanisms that control salt stress response in E. ulmoides.