Integrative RNA-Seq analysis of Capsicum annuum L . -Phytophthora capsici L. pathosystem reveals molecular cross-talk and activation of host defence response

Abstract Background Chili pepper ( Capsicum annuum L.) being one of an important member of the Solanaceae family, and its productivity is highly affected by the fungal pathogen Phytophthora capsici L. Other to CM-344, the unavailability of resistant landraces to all possible strains of P. capsici imposes a serious threat to its global production. This is because of our current understanding of the molecular mechanisms associated with the defence response in C. annuum - P. capsici pathosystem is limited. Therefore, the current study used RNA-seq technology to dissect the genes associated with defence response against P. capsici infection in two contrasting landraces, i.e. GojamMecha_9086 (Resistant) and Dabat_80045 (susceptible) exposed to P. capsici infection. Results The transcriptomes from 4 leaf samples (RC, RI, SC and SI) of chili pepper resulted in a total of 1,18, 879 assembled transcripts (with a mean TL of 813.23bp and N50 of 1,277bp) along with 52,384 pooled unigenes with (mean UL of 1029.36 bp and N50 of 1,403bp). The enrichment analysis of the transcripts indicated 23 different KEGG pathways under five main categories. Further, 774 and 484 differentially expressed genes (DEGs) were obtained from RC vs. RI and SC vs. SI leaf samples, respectively. Of these, 57 DEGs were found to be associated with defence responses against P. capsici infection. The defence-related genes, such as LTPL , defensin J1-2-like, peroxidase 5-like, UGT, and GRP proteins-like, were more significantly upregulated in RC vs. RI. Furthermore, RT-qPCR analysis of six randomly selected genes validated the results of Illumina NextSeq500 sequencing results. Furthermore, a total of 58 TF families (bHLH most abundant) and 2,095 protein families (Protein kinase, PF00069, most abundant) were observed across all the samples with maximum hits in RI and SI samples. Conclusions RNA-Seq analysis of chili pepper’s during P.capsici infection revealed differential regulation of genes associated with defence and signaling response with shared coordination of molecular function, cellular component and biological processing. The results presented here would enhance our present understanding of the defence response in chili pepper against P. capsici infection, which could be utilized by the molecular breeders to develop resistant chili genotypes.