title: Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses.
abstract: MicroRNAs (miRNAs) play a critical role in responses to biotic and abiotic stress and have been characterized in a large number of plant species. Although flax (Linum usitatissimum L.) is one of the most important fiber and oil crops worldwide, no reports have been published describing flax miRNAs (Lus-miRNAs) induced in response to saline, alkaline, and saline-alkaline stresses.
  
  
  
  In this work, combined small RNA and degradome deep sequencing was used to analyze flax libraries constructed after alkaline-salt stress (AS2), neutral salt stress (NSS), alkaline stress (AS), and the non-stressed control (CK). From the CK, AS, AS2, and NSS libraries, a total of 118, 119, 122, and 120 known Lus-miRNAs and 233, 213, 211, and 212 novel Lus-miRNAs were isolated, respectively. After assessment of differential expression profiles, 17 known Lus-miRNAs and 36 novel Lus-miRNAs were selected and used to predict putative target genes. Gene ontology term enrichment analysis revealed target genes that were involved in responses to stimuli, including signaling and catalytic activity. Eight Lus-miRNAs were selected for analysis using qRT-PCR to confirm the accuracy and reliability of the miRNA-seq results. The qRT-PCR results showed that changes in stress-induced expression profiles of these miRNAs mirrored expression trends observed using miRNA-seq. Degradome sequencing and transcriptome profiling showed that expression of 29 miRNA-target pairs displayed inverse expression patterns under saline, alkaline, and saline-alkaline stresses. From the target prediction analysis, the miR398a-targeted gene codes for a copper/zinc superoxide dismutase, and the miR530 has been shown to explicitly target WRKY family transcription factors, which suggesting that these two micRNAs and their targets may significant involve in the saline, alkaline, and saline-alkaline stress response in flax.
  
  
  
  Identification and characterization of flax miRNAs, their target genes, functional annotations, and gene expression patterns are reported in this work. These findings will enhance our understanding of flax miRNA regulatory mechanisms under saline, alkaline, and saline-alkaline stresses and provide a foundation for future elucidation of the specific functions of these miRNAs.
authors.affiliation: Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150086, People's Republic of China.|Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Guangwen
authors.initials: G
authors.lastname: Wu
authors.affiliation: Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150086, People's Republic of China.|Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Yuan
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Lili
authors.initials: L
authors.lastname: Cheng
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Wengong
authors.initials: W
authors.lastname: Huang
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Shuquan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China.
authors.forename: Liguo
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Division of Insect-borne Parastitic Disease Control and Prevention, Harbin Center for Disease Control and Prevention, Harbin, 150056, People's Republic of China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Chen
authors.affiliation: Alberta Innovates Technology Futures, Vegreville, Alberta, T9C 1 T4, Canada. jian.zhang@albertainnovates.ca.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, 150086, People's Republic of China. kj-gfz@163.com.|Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, People's Republic of China. kj-gfz@163.com.
authors.forename: Fengzhi
authors.initials: F
authors.lastname: Guan
mesh_terms: D000468:Alkalies / Q000378:metabolism*; D019597:Flax / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D012965:Sodium Chloride / Q000378:metabolism*; D013312:Stress, Physiological
chemical_list: D000468:Alkalies; D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D012965:Sodium Chloride
keywords: Deep sequencing; Degradome; Flax; MicroRNAs; Saline-alkaline stress