Establishment Of An Informatics Hub For Pepper-Pepperhub

Capsicum annuum L.is an important horticultural vegetable crop belonging to the same family of Solanaceae as tomato(Solanum lycopersicum L.),potato(Solanum tuberosum L.),and tobacco(Nicotiana tuberosum L.).Pepper have strong resistance to disease and stress,and they have strong adaptability to different agro-climatic conditions and are planted around the world.The content of vitamin C,vitamin A and vitamin B6 in pepper fruits is an important part of people's dietary nutrition.The shape,size,color,and taste of pepper fruits are rich and varied.This diversity makes them an important model for fruit developmental biology research.Compared with other solanaceous plants,capsicum has a large genome(about 3.3 Gb)and a high proportion of repeats(81%),difficulty in virus-induced gene silencing,and immature genetic transformation techniques.These limitations have caused slow progress in pepper-related research.In addition,the lack of a comprehensive pepper bioinformatics platform has to some extent hindered the study of chili pepperomics.Based on the previous results and the new sequencing data and analysis results of the research team,this study constructed the PepperHub pepper group biometric information platform.The main research results are as follows:1.Download the published genomic sequence and gene annotation files of CM334 pepper and Zunla pepper,assemble and annotate the capsicum genome data of the ?6421? strain obtained by pacbio third-generation resequencing,visualize the data of each group using the GBrowse gene browser,and combine the locally installed BLAST The tool and the established chili library build the Gemome module.2.Processing and analysis of the transcriptome data from different tissues at different developmental stages,after spraying various growth regulators,and different abiotic stresses.Based on data processing results,various types of software and written scripts are used to display the expression status of a gene at different developmental stages,after spraying growth regulators,and under different abiotic stresses in different tissues,and to compare the developmental status of two genes in different tissues at different developmental stages.Different expressions of exogenous hormones and different abiotic stresses were used to construct a co-expression network of a gene and its related genes.3.Prepare sRNA annotation files and miRNA annotation files using published pepper sRNA database and miRNA list,and use GBrowse to visualize the distribution of different pepper sRNA and known miRNA and novel miRNA in the genome.At the same time,a miRNA target gene database was constructed to search for a target gene with a specific name and a specific sequence of miRNAs in the pepper genome.4.Analyze and process the pepper genome resequencing data,identify the SNP and InDel loci of the capsicum genome,and use it to generate annotation files.Use GBrowse to read the annotation file and visualize the SNP and InDel loci.Establish SNP and InDel databases to query SNPs and InDels in specific regions.5.The use of HTML,CSS,JavaScript,Perl and other tools and languages to integrate various functional modules into a comprehensive pepper biological information platform-PeperHub.