Analyses of distal gene expression and proteome in developing tree peony seeds

Tree peony (Paeonia section Moutan DC.) seeds are an excellent source of effective constituents and oil content. In recent years, the tree peony has gained in popularity as a resource in food and nutraceutical industries. Therefore, understanding the transcriptional and translational regulation of seed formation is essential for increasing seed yields and modifying functional components by genetic engineering.In this study, we conducted analysis of distal gene expression and proteome at nine timepoints during the development of tree peony seeds, using a BGISEQ-500 RNA-seq platform and IBT technology. A total of 41808 unigenes were identified from 21.6 billion single-end 50 bp-long reads. Furthermore, 7026 peptides and 2841 proteins were screened out with the 1% false discovery rate (FDR). Our seed samples were divided into four developmental stages according to the cluster analysis of both differentially expressed genes (DEGs) and differentially expressed proteins (DEPs): 25–39 days after pollination (DAP; May 3, May 10 and May 17), 39–67 DAP (May 31 and Jun 14), 67–95 DAP (Jun 28, July 5 and July 12), and 95–109 DAP (July 26). The KEGG Orthology enrichment of DEGs and DEPs demonstrated that May 31 is the critical period for fatty acid biosynthesis and fatty acid metabolism, and alpha-linolenic acid (ALA) shows significant enrichment on July 26. We identified, via KEGG analysis, 211 genes and 35 proteins involved in fatty acid metabolism. By multiple reaction monitoring technology (MRM), the temporal expression patterns of DEPs related to fatty acid metabolism with high expression levels at the active stage of fatty acid metabolism rather than the initial stage of seed development were confirmed.This study provides the first conjoint distal gene expression and proteome analyses of principal molecular events and fatty acid metabolism during developing tree peony seeds. This data not only provide insight into the developmental mechanisms of tree peony seeds, but also reveal novel candidate genes which are worthy of further investigation into the value of genetic engineering of tree peony seeds.