title: Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum.
abstract: BACKGROUND
  Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Increasingly evidences suggest that long intergenic ncRNAs (lincRNAs) are developmentally regulated and play important roles in development and stress responses of plants. However, identification of lincRNAs in wheat is still limited comparing with functional gene expression.
  
  
  RESULTS
  The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR31 and Bgt race E09 at 1, 2, and 3 days post-inoculation was recapitulated to detect the lincRNAs. Here, 283 differential expressed lincRNAs were identified from 58218 putative lincRNAs, which account for 31.2% of transcriptome. Of which, 254 DE-LincRNAs responded to the Bgt stress, and 52 lincRNAs in Pst. Among them, 1328 SnRNP motifs (sm sites) were detected and showed RRU4-11RR sm site element and consensus RRU1-9VU1-7RR SnRNP motifs, where the total number of uridine was more than 3 but less than 11. Additionally, 101 DE-lincRNAs were predicted as targets of miRNA by psRNATarget, while 5 target mimics were identified using target mimicry search in TAPIR.
  
  
  CONCLUSIONS
  Taken together, our findings indicate that the lincRNA of wheat responded to Bgt and Pst stress and played important roles in splicesome and inter-regulating with miRNA. The sm site of wheat showed a more complex construction than that in mammal and model plant. The mass sequence data generated in this study provide a cue for future functional and molecular research on wheat-fungus interactions.
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China. zhangh1129@nwafu.edu.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.|National Laboratory of Wheat Engineering, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Jilei
authors.initials: J
authors.lastname: Hao
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Shikai
authors.initials: S
authors.lastname: Lv
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Changyou
authors.initials: C
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Wei
authors.initials: W
authors.lastname: Tong
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Yajuan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Yanzhen
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
authors.forename: Xinlun
authors.initials: X
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China. jiwanquan2008@126.com.
authors.forename: Wanquan
authors.initials: W
authors.lastname: Ji
mesh_terms: D001203:Ascomycota; D001487:Basidiomycota; D002874:Chromosome Mapping; D054884:Host-Pathogen Interactions; D035683:MicroRNAs / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D062085:RNA, Long Noncoding / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D059467:Transcriptome; D014908:Triticum / Q000235:genetics* / Q000382:microbiology
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D018749:RNA, Plant
keywords: Powdery mildew; RNA-Seq; Sm-site; Stripe rust; Wheat; lincRNA; miRNA target