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Background  As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to  Phytophthora capsici  is largely unknown.    Results  In this study, RNA-seq data of grafting and control pepper plants with or without  P .  capsici  inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between  P .  capsici  resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to  P .  capsici  by modulating the expression of disease-defense related genes through  cis -regulating and/or lincRNA-miRNA-mRNA interaction networks.    Conclusions  This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to  P .  capsici .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08183-z.

bmc genomics

Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici