title: NaCl stress-induced transcriptomics analysis of Salix linearistipularis (syn. Salix mongolica).
abstract: BACKGROUND
  Salix linearistipularis (syn. S. mongolica) is a woody halophyte, which is distributed naturally in saline-alkali soil of Songnen plain, Heilongjiang, China. It plays an important role in maintaining ecological balance and in improving saline soil. Furthermore, S. linearistipularis is also a genetic resource; however, there is no available information of genomic background for salt tolerance mechanism. We conducted the transcriptome analysis of S. linearistipularis to understand the mechanisms of salt tolerance by using RNA-seq technology.
  
  
  RESULTS
  The transcription profiles of both the salt stress (SLH-treated) and the control (SLH-control) sample for S. linearistipularis were obtained by using RNA-seq in this study. By comparative analysis, only 3034 of 53,362 all-unigenes between two samples were expressed differently at more than 1.5-fold ([Formula: see text], FDR ≤ 0.05), including 1397 up-regulated genes and 1637 down-regulated genes. In total, 2199 genes were classified into 50 Gene Ontology (GO) terms and 1103 genes were involved in 116 biological pathways. To find salt stress related genes, all-unigenes of S. linearistipularis were classified into three categories according to their degree of the differentially expressed genes (DEGs) at 0-1.5-fold (non differently expressed genes, N-DEGs), at 1.5-4.0-fold and more than 4.0-fold. The pathways of three categorized genes were compared with the DEGs of Arabidopsis thaliana, showing that 22, 10 and 1 pathway of S. linearistipularis were overlapped with A. thaliana. Degree of the overlapping was categorized as 0-1.5-fold, 1.5-4.0-fold and more than 4.0-folds.
  
  
  CONCLUSIONS
  Our study revealed that the N-DEGs of 22 pathways in S. linearistipularis were overlapped with the DEGs of A. thaliana. This result suggests that those overlapped genes that contrasted with the up- or down-regulated genes in A. thaliana were possibility evolved into housekeeping genes in S. linearistipularis under salt stress.
authors.affiliation: Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Hexing Road No. 26, Xiangfang, Harbin, 150040 Heilongjiang China ; College of Agriculture, Yanbian University, Yanji, 133002 China.
authors.forename: Guixian
authors.initials: G
authors.lastname: Nan
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081 China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081 China.
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.affiliation: Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Hexing Road No. 26, Xiangfang, Harbin, 150040 Heilongjiang China ; Institute of Physics, Nankai University, Nankai District, Tianjin, 300071 China.
authors.forename: Imshik
authors.initials: I
authors.lastname: Lee
authors.affiliation: Asian Natural Environment Science Center (ANESC), The University of Tokyo, Midori Cho 1-1-1, Nishitokyo, Tokyo 188-0002 Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Takano
authors.affiliation: Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Hexing Road No. 26, Xiangfang, Harbin, 150040 Heilongjiang China.
authors.forename: Shenkui
authors.initials: S
authors.lastname: Liu
keywords: Biological pathway; Differently expressed genes (DEGs); Non differently expressed genes (N-DEGs); RNA-Seq; Salix linearistipularis; Salt stress