Comprehensive Re-Annotation and Transcriptome Analysis Provide Insights into Pepper Development

Pepper (Capsicum annuum L.) is one of the most important vegetable crops with high nutritional, medicinal, and ornamental values. Genome decoding promotes pepper research, but the current annotation of gene structure in reference genomes is incomplete and inaccurate, hindering gene function study. Meanwhile, the gene regulatory modules that control pepper development need to be explored. To address these challenges, we conducted a comprehensive re-annotation of the gene structure in the pepper CA59 reference genome. The resulting v2a annotation demonstrated increased completeness and accuracy, with the completeness of BUSCO analysis increasing from 79.3 % to 98.9 %. Using this improved annotation, we investigated the transcriptome of pepper plants throughout their life cycle and identified 26,455 expressed genes, with 2990 genes showing specific expression in specific stages and 20,389 genes displaying differential expression across various developmental stages, highlighting the dynamic nature of gene expression in pepper. Through weighted gene co-expression network analysis (WGCNA), we identified organ-specific gene modules and constructed gene co-expression networks for leaves, flowers, seeds, and fruits, providing insights into the regulatory mechanisms governing organ development. This study offers valuable resources for future gene function research and genetic improvement of pepper.