Tree peony (Paeonia ostii) is an economically important ornamental plant native to China. It is also notable for its seed oil, which is abundant in unsaturated fatty acids such as α-linolenic acid (ALA). Here, we report chromosome-level genome assembly (12.28 Gb) ofP. ostii. In contrast to monocots with giant genomes, tree peony does not appear to have undergone lineage-specific whole-genome duplication. Instead, explosive LTR expansion in the intergenic regions within a short period (~ two million years) may have contributed to the formation of its giga-genome. In addition, expansion of five types of histone encoding genes may have helped maintain the giga-chromosomes. Further, we conduct genome-wide association studies (GWAS) on 448 accessions and show expansion and high expression of several genes in the key nodes of fatty acid biosynthetic pathway, includingSAD,FAD2andFAD3, may function in high level of ALAs synthesis in tree peony seeds. Moreover, by comparing with cultivated tree peony (P. suffruticosa), we show that ectopic expression of class A geneAP1and reduced expression of class C geneAGmay contribute to the formation of petaloid stamens. Genomic resources reported in this study will be valuable for studying chromosome/genome evolution and tree peony breeding.

Most common plant oils have little α-linolenic acid (C18:3^Δ9,12,15, ALA) and an unhealthy ω6/ω3 ratio. Here, fatty acids (FAs) in the seeds of 11 species of Paeonia L., including 10 tree peony and one herbaceous species, were explored using gas chromatograph–mass spectrometer. Results indicated that all Paeonia had a ω6/ω3 ratio less than 1.0, and high amounts of ALA (26.7–50%), oleic acid (C18:1^Δ9, OA) (20.8–46%) and linoleic acid (C18:2^Δ9,12, LA) (10–38%). ALA was a dominant component in oils of seven subsection Vaginatae species, whereas OA was predominant in two subsection Delavayanae species. LA was a subdominant oil component in P. ostii and P. obovata. Moreover, the FA composition and distribution of embryo (22 FAs), endosperm (14 FAs) and seed coat (6 FAs) in P. ostii, P. rockii and P. ludlowii were first reported. Peony species, particularly P. decomposita and P. rockii, can be excellent plant resources for edible oil because they provide abundant ALA to balance the ω6/ω3 ratio. The differences in the ALA, LA and OA content proportion also make the peony species a good system for detailed investigation of FA biosynthesis pathway and ALA accumulation.

Tree peonies are a group of traditional ornamental plants, especially in East Asia, with Paeonia ostii as one of the most important ancestral species. P. ostii has flowers with varying colors, ranging from nearly white, light pink to deep pink. However, few studies have been done to unravel the molecular mechanisms underlying the flower color intensity variation in plants. Based on comparative analyses of the pigment composition and transcriptomes of P. ostii with different flower color intensities, we found that the anthocyanin concentration was significantly correlated with the flower color intensity in P. ostii. Transcriptome analysis by RNA-Sequencing revealed 7,187 genes that were differentially expressed between flowers with different color intensities. Functional enrichment analysis of differentially expressed genes revealed multiple pathways possibly responsible for color intensity variation in P. ostii, including flavonoid biosynthesis, fatty acid oxidation, carbohydrate metabolism and hormone-mediated signaling. Particularly, while anthocyanin biosynthesis genes showing positive correlations between their expression and anthocyanin concentration in flowers, two transcription factors, PoMYB2 and PoSPL1, seem to negatively regulate anthocyanin accumulation by affecting the activation capacity of the MYB-bHLH-WDR complex, exhibiting an inverse relationship between their expression and anthocyanin accumulation. Our results showed that, although anthocyanin biosynthesis had a direct effect on the pigmentation of the P. ostii flower, other metabolic and hormone-mediated signaling pathways were also contributed to the flower color intensity variation in P. ostii, suggesting complex coordinated changes in the transcriptional network. Differential expression of genes encoding anthocyanin repressors seems to be the major factor responsible for the intensity variation in anthocyanin pigmentation in P. ostii.

Tanshinone ⅡA (TⅡA), a diterpene quinone with a furan ring, is a bioactive compound found in the medicinal herb redroot sage (Salvia miltiorrhiza Bunge), in which both furan and dihydrofuran analogs are present in abundance. Progress has been made recently in elucidating the tanshinone biosynthetic pathway, including heterocyclization of the dihydrofuran D-ring by cytochrome P450s; however, dehydrogenation of dihydrofuran to furan, a key step of furan ring formation, remains uncharacterized. Here, by differential transcriptome mining, we identified six 2-oxoglutarate-dependent dioxygenase (2-ODD) genes whose expressions corresponded to tanshinone biosynthesis. We showed that Sm2-ODD14 acts as a dehydrogenase catalyzing the furan ring aromatization. In vitro Sm2-ODD14 converted cryptotanshinone to TⅡA and thus was designated TⅡA synthase (SmTⅡAS). Furthermore, SmTⅡAS showed a strict substrate specificity, and repression of SmTⅡAS expression in hairy root by RNAi led to increased accumulation of total dihydrofuran-tanshinones and decreased production of furan-tanshinones. We conclude that SmTⅡAS controls the metabolite flux from dihydrofuran- to furan-tanshinones, which influences medicinal properties of S. miltiorrhiza.

Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double membrane–bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected, owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated and processed via the CHLORAD pathway: They are degraded by the 26 S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically derived chloroplasts, where it acts to regulate photosynthesis, arguably the most fundamental process of life.