Transcriptomic analysis of α-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds

The chromosome-level genome of Eucommia ulmoides provides insights into sex differentiation and α-linolenic acid biosynthesis

Eucommia ulmoides Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of E. ulmoides obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that E. ulmoides has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, EuAP3 and EuAG may be the key genes involved in regulating the sex differentiation of E. ulmoides. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene EU0103017 was an important reason for the high α-linolenic acid content in E. ulmoides. The genome of female and male E. ulmoides presented here is a valuable resource for the molecular biological study of sex differentiation of E. ulmoides and also will provide assistance for the breeding of superior varieties.

DUS evaluation of nine intersubgeneric hybrids of Paeonia lactiflora and fingerprint analysis of the chemical components in the roots

Intersubgeneric hybrids of Paeonia lactiflora (Paeonia lactiflora pall., P. lactiflora.) cover a huge variety of systems in the genus Paeonia. In recent years, many studies have confirmed that the intersubgeneric hybrids of P. lactiflora. are rich in paeoniflorin and other medicinal ingredients, however, it has always proved difficult to clarify the medicinal value of the hybrids and whether they can be used for medicinal purposes. In this study, the consistency of the plant population was evaluated through DUS evaluation, in order to clarify whether the selected research materials had stability and consistency within the population and specificity between populations. The differences between the paeoniflorin contents in the roots of the nine intersubgeneric hybrids of the P. lactiflora. varieties and two medicinal varieties were critically compared. The differences in the chemical components of the roots of nine intersubgeneric hybrids of P. lactiflora. and reference medicine substances of P. lactiflora. and Paeonia anomala subsp. veitchii (Lynch) D. Y. Hong and K. Y. Pan (Paeonia veitchii Lynch., P. veitchii.) were explored via stoichiometric and chemical fingerprint high performance liquid chromatography analyses. The results showed that there were significant differences in the chemical compositions between the intersubgeneric hybrids of P. lactiflora. and the medicinal reference materials, and the contents of paeoniflorin were elevated such that the hybrids could be used as the raw material for extraction of paeoniflorin, thus providing an opportunity to explore the medicinal value of the hybrids. This study explored the key differential components among the varieties and provides a reference and basis for the study of the medicinal value and the identification of the intersubgeneric hybrids of the P. lactiflora. varieties.

Transcriptome Analysis of Genes Involved in Fatty Acid and Lipid Biosynthesis in Developing Walnut (Juglans regia L.) Seed Kernels from Qinghai Plateau

Walnut (Juglans regia) is an important woody oil-bearing plant with high nutritional value. For better understanding of the underlying molecular mechanisms of its oil accumulation in the Qinghai Plateau, in this study we monitored walnut fruit development, and 15 cDNA libraries were constructed from walnut seed kernels collected at 72, 79, 93, 118 and 135 days after flowering (DAF). The candidate genes were identified using sequencing and expression analysis. The results showed that the oil content in the kernels increased dramatically in late July and reached the maximum value of 69% in mature seed. More than 90% of the oils were unsaturated fatty acids (UFAs) and linoleic acid (18:2) was the predominant UFA accumulated in mature seed. Differentially expressed genes (DEGs) in 15 KEGG pathways of lipid metabolism were detected. We identified 119 DEGs related to FA de novo biosynthesis (38 DEGs), FA elongation and desaturation (39 DEGs), triacylglycerol (TAG) assembly (24 DEGs), oil bodies (12 DEGs), and transcription factors (TFs, 6 DEGs). The abundantly expressed oleosins, caleosins and steroleosins may be important for timely energy reserve in oil bodies. Weighted gene coexpression network analysis (WGCNA) showed that AP2/ERF and bHLH were the key TFs, and were co-expressed with ACC1, α-CT, BCCP, MAT, KASII, LACS, FATA, and PDCT. Our transcriptome data will enrich public databases and provide new insights into functional genes related to the seed kernel lipid metabolism and oil accumulation in J. regia.

Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages

Background

Armeniaca sibirica seed kernel oil is rich in oleic acid and linoleic acid, thus holding potential value as a source of high-quality edible oils. However, some regulatory factors involved in fatty acids accumulation in A. sibirica seed kernels remain largely elusive. Thus, the aim of this study was to elucidate the regulatory mechanisms underlying fatty acids biosynthesis in A. sibirica developing seed kernels.

Methods

Seed kernels from six plants from a single A. sibirica clone were taken at five different developmental stages (days 30, 41, 52, 63, and 73 after anthesis). Fatty acid composition in seed kernel oil was determined by gas chromatography-mass spectrometry (GC-MS). In addition, transcriptome analysis was conducted using second-generation sequencing (SGS) and single-molecule real-time sequencing (SMRT).

Results

Rapid accumulation of fatty acids occurred throughout the different stages of seed kernels development, with oleic acid and linoleic acid as the main fatty acids. A total of 10,024, 9,803, 6,004, 6,719 and 9,688 unigenes were matched in the Nt, Nr, KOG, GO and KEGG databases, respectively. In the category lipid metabolism, 228 differentially expressed genes (DEGs) were annotated into 13 KEGG pathways. Specific unigenes encoding 12 key enzymes related to fatty acids biosynthesis were determined. Co-expression network analysis identified 11 transcription factors (TFs) and 13 long non-coding RNAs (lncRNAs) which putatively participate in the regulation of fatty acid biosynthesis. This study provides insights into the molecular regulatory mechanisms of fatty acids biosynthesis in A. sibirica developing seed kernels, and enabled the identification of novel candidate factors for future improvement of the production and quality of seed kernel oil by breeding.

Iso-Seq and RNA-Seq analyses uncover the molecular response of Dalbergia odorifera T. Chen to low temperature

In previous studies, we found young plants propagated from acclimated D. odorifera T. Chen trees displayed increased cold tolerance. To understand the molecular and physiological mechanisms underlying this phenomenon, we prepared acclimated and non-acclimated young D. odorifera T. Chen trees for physiological, RNA-Seq, and Iso-Seq analyses. First, both the acclimated and non-acclimated young trees were grown in 10 ℃ condition, then treated at -3 ℃ for one day, and finally recovered at 10 ℃. The measurement of physiological parameters, including superoxide dismutase, peroxidase, malondialdehyde, thiobarbituric acid, and soluble sugar, showed that the physiological change of acclimated plants is smoother than non-acclimated plants. The RNA-Seq analyses pointed out that cold acclimation already fixed the different gene expression patterns of D. odorifera T. Chen trees. The hormone-related, secondary metabolic, and signal transduction related biological genes tend to show different expressions between the acclimated and non-acclimated D. odorifera T. Chen trees. Moreover, the change of gene expression for some biological processes, such as alpha-Linolenic acid metabolism and its response to hydrogen peroxide, seems to occur earlier in non-acclimated than acclimated plants. The ISO-Seq analyses pointed out that alternative splicing (AS) of some genes was also found, and these AS events were predicted to play important roles in regulating different expression patterns between non-acclimated and acclimated plants. Therefore, according to the performance of this study, we are able to provide some novel understanding of cold tolerance enhanced by cold acclimation in perennial trees.

Overexpression of PvFAD3 Gene from Plukenetia volubilis Promotes the Biosynthesis of α-Linolenic Acid in Transgenic Tobacco Seeds

The ω-3 fatty acid desaturase (FAD3) gene encodes a rate-limiting enzyme in the synthesis of α-linolenic acid. In this study, homologous cloning was used to obtain the full-length sequence of the PvFAD3 gene of Plukenetia volubilis. The full-length DNA sequence was 1871 bp long, with 8 exons and 7 introns. The structural analysis of the amino acid sequence revealed that the PvFAD3 protein contained three histidine-conserved regions and an endoplasmic reticulum retention signal. The real-time reverse transcription-polymerase chain reaction performed for determining the expression patterns of the PvFAD3 gene in different tissues of P. volubilis showed that PvFAD3 expression was highly expressed in the fast oil accumulation stage of seed. The analysis of subcellular localization assay in epidermal cells of tobacco (Nicotiana benthamiana) leaves showed that the PvFAD3 protein was mainly localized in the endoplasmic reticulum. Seed-specific overexpression vectors were constructed, and Agrobacterium-mediated genetic transformation was performed to obtain transgenic tobacco plants overexpressing PvFAD3. The results of fatty acid assays performed using harvested seeds showed a significant increase in α-linolenic acid content, a dramatic decrease in linoleic acid content, and an obvious increase in oil content in transgenic tobacco seeds. Collectively, the PvFAD3 gene of P. volubilis was confirmed as a key enzyme gene for α-linolenic acid synthesis; thus, indicating that the PvFAD3 gene can be used for fatty acid fraction improvement in oilseed plants.