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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.

Elymus nutans is an important forage and ecological restoration herbage in the Qinghai-Tibet Plateau, which is an allohexaploid species with the StStYYHH genomes. Previous studies suggested that Pseudoroegneria is the maternal genome donor to E. nutans, but exactly which Pseudoroegneria species is still unknown. Here, we report the complete chloroplast (cp) genome sequence of two E. nutans from the Qinghai-Tibet and five Pseudoroegneria species. The cp genomes of the seven samples ranged narrowly from 134,924 bp to 135,142 bp in size, comprising inverted repeats of 20,808-20,814 bp, single-copy regions of 80,536-80,754 bp (LSC) and 12,762-12,772 bp (SSC). It encoded 111 total genes, of which 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. A comparative cp genome analysis and characteristic junctions of St-containing species revealed that the gene content and organization were conserved, but differences were still found in sequence variation and border regions. Further, the Bayesian inference (BI) phylogenetic tree using the whole chloroplast genome sequence demonstrated that P. cognata might be the most likely St genome donor of E. nutans in the Qinghai-Tibet Plateau, followed by P. strigosa. However, whether E. nutans has other maternal genomes still needs further research.

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