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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 RRU 4–11 RR sm site element and consensus RRU 1–9 VU 1–7 RR 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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2570-0) contains supplementary material, which is available to authorized users.

Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum