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Abstract Background Paeonia lactiflora ‘Hangshao’ is widely cultivated in China as a traditional Chinese medicine ‘Radix Paeoniae Alba’. Due to the abundant unsaturated fatty acids in its seed, it can also be regarded as a new oilseed plant. However, the process of the biosynthesis of unsaturated fatty acids in it has remained unknown. Therefore, transcriptome analysis is helpful to better understand the underlying molecular mechanisms. Results Five main fatty acids were detected, including stearic acid, palmitic acid, oleic acid, linoleic acid and α-linolenic acid, and their absolute contents first increased and then decreased during seed development. A total of 150,156 unigenes were obtained by transcriptome sequencing. There were 15,005 unigenes annotated in the seven functional databases, including NR, NT, GO, KOG, KEGG, Swiss-Prot and InterPro. Based on the KEGG database, 1766 unigenes were annotated in the lipid metabolism. There were 4635, 12,304, and 18,291 DEGs in Group I (60 vs 30 DAF), Group II (90 vs 60 DAF) and Group III (90 vs 30 DAF), respectively. A total of 1480 DEGs were detected in the intersection of the three groups. In 14 KEGG pathways of lipid metabolism, 503 DEGs were found, belonging to 111 enzymes. We screened out 123 DEGs involved in fatty acid biosynthesis (39 DEGs), fatty acid elongation (33 DEGs), biosynthesis of unsaturated fatty acid (24 DEGs), TAG assembly (17 DEGs) and lipid storage (10 DEGs). Furthermore, qRT-PCR was used to analyze the expression patterns of 16 genes, including BBCP, BC, MCAT, KASIII, KASII, FATA, FATB, KCR, SAD, FAD2, FAD3, FAD7, GPAT, DGAT, OLE and CLO, most of which showed the highest expression at 45 DAF, except for DGAT, OLE and CLO, which showed the highest expression at 75 DAF. Conclusions We predicted that MCAT, KASIII, FATA, SAD, FAD2, FAD3, DGAT and OLE were the key genes in the unsaturated fatty acid biosynthesis and oil accumulation in herbaceous peony seed. This study provides the first comprehensive genomic resources characterizing herbaceous peony seed gene expression at the transcriptional level. These data lay the foundation for elucidating the molecular mechanisms of fatty acid biosynthesis and oil accumulation for herbaceous peony.

The flower-meristem-identity gene APETALA2 (AP2), one of class-A genes, is involved in the establishment of the floral meristem and the forming of sepals and petals. Codon usage bias (CUB) identifies differences among species, meanwhile dynamic analysis of base composition can identify the molecular mechanisms and evolutionary relationships of a specific gene. In this study, eight coding sequences (CDS) of AP2 gene were selected from different plant species using the GenBank database. Their nucleotide composition (GC content), genetic index, relative synonymous codon usage (RSCU) and relative codon usage bias (RCUB) were calculated with R Software to compare codon bias and base composition dynamics of AP2 gene codon usage patterns in different plant species. The results showed that the usage of AP2 gene codons from different plant species were influened by GC bias, especially GC3s. Overall, base composition analysis indicated that the usage frequency of codon AT in the gene coding sequence was higher than GC among AP2 gene CDS from different plant species. Furthermore, most AP2 gene CDSs ended with AT; AGA, GCU and UGU had relatively high RSCU values as the most dominant codon; the usage characteristic of the AP2 gene codon in Malus domestica was similar to that of Vitis vinifera; Paeonia lactiflora was similar to Paeonia suffruticosa and Solanum lycopersicum was similar to Petunia×hybrida. There was a moderate preference in the usage of AP2 gene codon among different plant species from relatively low frequency of optimal codon (Fop) values and high effective number of codons (ENC) value. This study has revealed the usage characteristics of the AP2 gene codon from the comparision of AP2 gene codon preference and base dynamics in different plant species and provide a platform for further study towards transgenic engineering and codon optimization.

Chalcone isomerase (CHI) is a key enzyme that converts yellow chalcone to colorless naringenin, playing an important regulatory role in color formation of ornamental flowers. We determined the coding sequence of CHI in herbaceous peony using rapid-amplification of cDNA ends (RACE) technology, and subsequently detected the expression pattern of CHI in the inner and outer petals at different developmental stages using qRT-PCR. We cloned the upstream promoter sequences of CHI using genome walking technology and predicted the location of CpG islands and 5′ truncation. In addition, we constructed five dual-luciferase reporter gene carriers and detected the promoter activities of different fragments. Our results showed that the full-length cDNA sequence of CHI was 898 bp, and the 5′-upstream core promoter was located at −1651 to −2050 bp region, where contained one CpG island (−1897 to −2010 bp) and several important binding sites of transcription factor, such as Sp1, serum response factor (SRF), activating protein (AP)-2alpha and CCAAT/enhancer binding protein (C/EBP)alpha. Expression results showed that the expression of CHI at different developmental stages was generally higher in inner petals than those in outer petals, and the maximum at the bud stage (S1). Thus, this study will provide theoretical basis for an in-depth study of CHI gene function and expression regulation.

Herbaceous peony (Paeonia lactiflora Pall.) is a famous flower with medicinal values, and its flowers have a number of medicinal constituents, especially flavonoids. In this study, a P. lactiflora cultivar with double colors including white outer-petal and yellow inner-petal was used as the experimental materials to perform the qualitative and quantitative analysis of flavonoids by high-performance liquid chromatograph-electrospray ionization-mass spectrometry (HPLC-ESI-MSn) and investigate the expression patterns of flavonoid biosynthetic genes using real-time quantitative polymerase chain reaction (Q-PCR). The results showed that the colors of both petals gradually weakened with flower development. Moreover, one main anthocyanin composition (peonidin 3,5-di-O-glucoside) and five main anthoxanthin compositions (kaempferol di-hexo-side, kaempferol-3-O-malonylglucoside-7-O-glucoside, quercetin-3-O-galactoside, luteolin-7-O-glucoside and isorhamnetin-3-O-glucoside) were found in the both, differing significantly in their peak areas only. Total anthocyanin, anthoxanthin and flavonoid contents in white outer-petal and yellow inner-petal gradually decreased during flower development, and were consistently higher in white outer-petal. Furthermore, the expression patterns of nine structural genes in P. lactiflora flavonoid biosynthetic pathway showed that the expression levels of phenylalanine ammonialyase gene (PIPAL), chalcone synthase gene (PICHS), flavanone 3-hydroxylase gene (PIF3H), anthocyanidin synthase gene (PIANS) and UDP-glucoside: flavonoid 5-O-glucosyltransferase gene (PIF5GT) in two petals basically presented declined tendencies, and transcription levels of PIPAL, PICHS, PIANS, PIF3GT and PIF5GT also tended to be higher in white outer-petal, which was correlated with their flavonoid contents. These results would lay a solid foundation for the exploration and utilization of flavonoid resources in P. lactiflora flowers.

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Herbaceous peony (Paeonia lactiflora Pall.) is an excellent material for studying the formation of flower colour because of its abundant colour. The full-length cDNA of a UDP-glucose: Flavonoid 5-O-glucosyltransferase gene (UF5GT) containing 1629 bp nucleotides was obtained from P. lactiflora. The expression patterns of nine related anthocyanin biosynthetic genes (PlPSY, PlCHS, PlCHI, PlF3H, PlF3'H, PlDFR, PlANS, PlUF3GT and PlUF5GT) in diurnal variation petals showed that their expression peaks were basically at 15:00 and the expression patterns were consistent with the trend of sampling conditions except individual gene. And the highest expression levels were in PlCHS, PlDFR and PlUF3GT, which could be the candidates to regulate P. lactiflora flower colour by means of genetic engineering [ABSTRACT FROM AUTHOR]