Ankita Negi

Black pepper (Piper nigrum, 2n = 52), an important spice, has been traditionally used for the treatment of various diseases owing to its therapeutic properties since time immemorial. Antimicrobial peptides (AMPs) (nature's antibiotics/host defense peptides) are produced by living organisms as innate immune response against microbes. To overcome the problem of antimicrobial resistance (AMR), toxicity residue of antibiotics and more, the computational approach tuning to AMPs prediction and whole genome analysis will be advantageous. In this work, in silico prediction of genome-wide AMPs in black pepper and development of its specific prediction server using machine learning techniques were done along with identification of molecular markers and miRNAs in black pepper genome. Web genomic resources, including species-specific AMP candidate prediction server BPepAMPred (http://login1.cabgrid.res.in:5040/) based on bidirectional- Gated Recurrent Unit- based deep neural network architecture, BPepAMPdb (http://backlin.cabgrid.res.in/blackpepper_amp_db/) cataloguing predicted 43759 AMP candidates across black pepper proteome along with 10935 functionally associated unique genes with detailed features were developed. BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), which is the first largest reported web resource for black pepper genomic SSRs and polymorphic SSRs was also developed using ddRAD GBS data of 29 genotypes of black pepper across India were used. A total of 276230 genomic SSRs with average distance of 2.76 Kb between each SSR and a relative density of 362.88 SSRs per Mb, 3176 polymorphic SSRs from 29 black pepper genotypes, out of which 2015 were found hypervariable. The study also reports 2029 putative conserved miRNAs and 4207 miRNA targets coding sequences of black pepper which were functionally characterised to determine the possible post-transcriptional regulatory processes. This information can be used by researchers for the study of genetic diversity among the different black pepper verities, studies of post-transcriptional regulation and its role in various black pepper diseases. The markers provided can be used in QTL discovery, variety signature, traceability of produce and product, including GI certification if needed and in improvement program.