Conjoint transcriptomic and proteogenomic analysis of quality formation in various Porphyra dentata harvests: Photosynthesis acts as a stressor

Porphyra dentata is widely cultivated for its rich nutritional value and superior palatability. However, its quality varies with harvest time and there is a lack of understanding of the molecular mechanism of quality differences. Photosynthesis is a key factor in human-mediated plant development and quality formation and changes. To explore the quality impact of photosynthesis on P. dentata, we compared transcriptomic and proteogenomic data of the first and fifth harvests. Of the 53,580 genes detected in this study, 7073 were identified as differentally expressed genes by RNA-seq, and 462 showed differential expression between genes and proteins in proteogenomics. The results show that quality differences between harvest periods were regulated by proteins and genes from the allophycocyanin, Lhca1, chloroplast processing enzyme, and phycocyanin families. Generated cell tissue passivated continuously, the blades gradually became thicker and darker and had an increased degree of lignification, decreased protein levels, increased carbohydrate levels, and decreased quality. Our results demonstrate the complementary power of transcriptomics and proteogenomics and provide a rich database for quality improvement or evolutionary function analysis of P. dentata.