Comparative transcriptomic analysis reveals genes related to the rapid accumulation of oleic acid in Camellia chekiangoleosa, an oil tea plant with early maturity and large fruit

The scent of time: Analyzing the differences in volatile organic compounds of camellia oleifera oil with different oil-tea tree ages using GC-IMS and GC-MS

Camellia oleifera oil (CO) is renowned in China for its exceptional nutritional benefits and distinctive aroma. The aroma of old CO from oil-tea tree ages over 30 years differs markedly from that of young CO aged below 8 years. However, the volatile organic compounds (VOCs) and aroma characteristics of CO from oil-tea tree at different ages remain unclear. This study identified 82 VOCs using GC-IMS and 112 VOCs using GC-MS. PCA, PLS-DA, correlation analysis, and VIP values revealed distinct VOC profiles between CO obtained from young and old oil-tea tree. The principal characteristic VOCs of CO from young oil-tea tree (4 and 8 years) were 3-methyl-3-buten-1-ol (sweet fruit) and 3-methylbutyl propanoate (apple, apricot, and pineapple). Moreover, the predominant characteristic VOCs of CO from old oil-tea tree (30, 40, and 50 years) were 4-methyl-2-pentanol (pungent), butyl acetate (apple and banana), limonene (lemon and orange), and 2-ethyl-6-methylpyrazine (green, nuts, and roasted).

The developmental transcriptome dynamics of current-year shoot utilized as scion in Camellia chekiangoleosa

BACKGROUND

Camellia chekiangoleosa is the most widely planted red-flowered and large-fruited oil-camellia species, with high value in edible oil production and landscaping. To better understand the weak scion development and slow graft-union healing underlying grafting propagation challenges in C. chekiangoleosa, we conducted temporal RNA-seq on current-year shoots with five time points determined according to changes in cell wall composition, aiming to reveal dynamic developmental regulation.

RESULTS

Analysis of temporal expression characteristics of genome-wide genes and differentially expressed genes (DEGs) revealed that genes differentially patterned between stem and apical bud were enriched in functions related to cell division and differentiation, hormone responses, and vascular or flower development. Coexpression network analysis revealed that red/far-red light and gibberellin (GA) signaling were closely correlated with flowering development in C. chekiangoleosa shoots. We further analyzed a unique module showing a negative correlation between the module and traits (cell wall composition, i.e., lignin, cellulose, and hemicellulose content). Genes in the top-scored sub-cluster of this module were enriched in shoot development-related processes, including cell wall dynamics, xylem development, secondary cell wall biogenesis, lignin biosynthesis, and procambium histogenesis. WOX4 and PXY, known markers of cambium cells, were identified as key hub genes, along with the actin-binding protein WLIM1. These coexpressed hub genes associated with vascular system development peaked in June in stems and were validated by qRT-PCR, suggesting that June may be an optimal grafting season for C. chekiangoleosa.

CONCLUSIONS

Integrating transcriptomics and physiology defined the dynamic signature of changes in composition of cell wall and gene activity during the development of current-year shoots in C. chekiangoleosa. Our findings provide insights into a potential molecular strategy for breeders, targeting key regulators specific to cambium differentiation, and physiological strategy for hormone or light supplied artificially to enhance grafting productivity of C. chekiangoleosa.

Genome-Wide Analyses of MADS-Box Genes Reveal Their Involvement in Seed Development and Oil Accumulation of Tea-Oil Tree (Camellia oleifera)

The seeds of Camellia oleifera produce high amount of oil, which can be broadly used in the fields of food, industry, and medicine. However, the molecular regulation mechanisms of seed development and oil accumulation in C. oleifera are unclear. In this study, evolutionary and expression analyses of the MADS-box gene family were performed across the C. oleifera genome for the first time. A total of 86 MADS-box genes (ColMADS) were identified, including 60 M-type and 26 MIKC members. More gene duplication events occurred in M-type subfamily (6) than that in MIKC subfamily (2), and SEP-like genes were lost from the MIKCC clade. Furthermore, 8, 15, and 17 differentially expressed ColMADS genes (DEGs) were detected between three developmental stages of seed (S1/S2, S2/S3, and S1/S3), respectively. Among these DEGs, the STK-like ColMADS12 and TT16-like ColMADS17 were highly expressed during the seed formation (S1 and S2), agreeing with their predicted functions to positively regulate the seed organogenesis and oil accumulation. While ColMADS57 and ColMADS07 showed increasing expression level with the seed maturation (S2 and S3), conforming to their potential roles in promoting the seed ripening. In all, these results revealed a critical role of MADS-box genes in the C. oleifera seed development and oil accumulation, which will contribute to the future molecular breeding of C. oleifera.

Full-length transcriptome sequencing provides new insights into the complexity of flavonoid biosynthesis in Glechoma longituba

Glechoma longituba has been frequently used in treating urolithiasis and cholelithiasis due to the presence of flavonoids, which are its major bioactive constituents. However, research on the molecular background of flavonoid biosynthesis in G. longituba is limited. In this study, we used single-molecule real-time combined with next-generation sequencing technologies to construct the complete transcriptome of G. longituba. We identified 404,648 non-redundant transcripts, including 249,697 coding sequences, 197,811 simple sequence repeats, 174,846 long noncoding RNA, and 176,554 coding RNA. Moreover, we functionally annotated 346,218 isoforms (85.56%) and identified 86,528 differentially expressed genes. We also identified 55 non-redundant full-length isoforms related to the flavonoid biosynthetic pathway. Pearson correlation analysis revealed that the expression levels of some key genes of the flavonoid biosynthesis pathway were significantly positively correlated with the flavonoid metabolites. Furthermore, we performed bioinformatics analysis (sequence and structural) of isoform_47029 (encoding flavanone 3-hydroxylase) and isoform_53692 (encoding flavonol synthase) to evaluate their potential biological functions. Finally, we validated gene expression levels of 12 flavonoid-related key enzyme genes using quantitative real-time PCR. Overall, this study provides full-length transcriptome information on G. longituba for the first time and valuable molecular resources for further research on the medicinal properties of this plant.

Lipidomic and comparative transcriptomic analysis of fatty acid synthesis pathway in Carya illinoinensis embryo

Pecan (Carya illinoinensis (Wagenh.) K. Koch) is an important oilseed nut and is rich in fatty acids (FAs) and flavonols. Pecan FA has significantly edible, industrial and clinical value. To investigate the dynamic patterns and compositions of FA, and the molecular mechanism that controls FA accumulation in pecan, lipidomic and transcriptomic analyses were performed to determine lipid profiles and gene expression in pecan's FA biosynthesis pathway. In the present study, compared with cultivars 'Caddo' and 'Y-01', 'Mahan' formed larger and heavier embryos and accumulated higher oil content. Lipidomic analysis showed that FA and (O-acyl)-1-hydroxy FA contents were higher in 'Mahan' at the mature stage. Based on full-length and comparative RNA-Seq, differential expression gene enrichment analysis revealed that many functional genes participated in the pathways of 'fatty acid biosynthesis', 'fatty acid metabolism' and 'linoleic acid metabolism'. High FA accumulation model from 'Mahan' demonstrated that key enzyme-encoding genes played an important role in regulating FA biosynthesis. Co-expression module analysis indicated that several transcription factors (TFs; MYB, TCP, bHLH, Dof, ERF, NAC) were involved in FA accumulation by regulating the expression of functional genes, and real-time quantitative PCR verification proved that these TFs had a high correlation with the pecan FA accumulation pattern. These findings provided an insight into the molecular mechanism of FA accumulation in C. illinoinensis embryo, which contributes to pecan oil yielding and pecan molecular breeding.

Comprehensive Evaluation of Quality Characteristics of Four Oil-Tea Camellia Species with Red Flowers and Large Fruit

Red-flowered oil-tea camellia (ROC) is an important woody oil species growing in the south, and its oil has high nutritional value. There are four main species of ROC in China, namely, Camellia chekiangoleosa (CCH), Camellia polyodonta (CPO), Camellia semiserrata (CSE) and Camellia reticulata (CRE). Reports on the comprehensive comparative analysis of ROC are limited. This study investigated the fruit characteristics and nutritional components of four ROC fruits, and the results showed that ROC had high oil content with levels of 39.13%-58.84%, especially the CCH fruit, which reached 53.6-58.84%. The contents of lipid concomitants of ROC oil were also substantial, including β-amyrin (0.87 mg/g-1.41 mg/g), squalene (0.43 mg/g-0.69 mg/g), β-sitosterin (0.47 mg/g-0.63 mg/g) and α-tocopherol (177.52 μg/g-352.27 μg/g). Moreover, the transverse diameter(TD)/longitudinal diameter (LD) of fruits showed a significant positive correlation with the oil content, and ROC fruits with thinner peels seemed to have better oil quality, which is similar to the result of the oil quality evaluation obtained by the gray correlation coefficient evaluation method. Four ROC oils were evaluated using the gray correlation coefficient method based on 11 indicators related to the nutritional value of ROC. CCH oil had the highest score of 0.8365, and YS-2 (a clone of CCH) was further evaluated as the best CCH oil. Finally, the results of heatmap analysis showed that triglycerides could be used as a characteristic substance to distinguish CCH oil from the other three ROC oils. The PLSDA (Partial least squares regression analysis) model and VIP (Variable important in projection) values further showed that P/S/O, P/O/O, P/L/L, P/L/Ln, S/S/O, S/O/O and P/S/S (these all represent abbreviations for fatty acids) could be used as characteristic differential triglycerides among the four ROC oils. This study provides a convenient way for planters to assess the nutritional quality of seed oil depending on fruit morphology and a potential way to distinguish between various ROC oils.

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Camellia chekiangoleosa is a popular variety of Oil-camellia that has high oil production and ornamental value. Microsatellite (SSR) markers are the preferred tool for the molecular marker-assisted breeding of C. chekiangoleosa. By focusing on the problems of the low development efficiency of polymorphic SSR markers and the lack of available functional markers in Oil-camellia, we identified 97,510 SSR loci based on the full-length transcriptome sequence of C. chekiangoleosa. An analysis of SSR characteristics showed that mononucleotide (51.29%) and dinucleotide (34.36%) SSRs were the main repeat types. The main SSR distribution areas based on proportion covered were ordered as follows: 5'UTR > 3'UTR > CDS. By comparing our data with those in databases such as GO and KEGG, we obtained functional annotations of unigene sequences containing SSR sites. The data showed that the amplification efficiency of the SSR primers was 51.72%, and the development efficiency of polymorphic SSR primers was 26.72%. Experiments verified that dinucleotide and pentanucleotide SSRs located in UTR regions could produce more polymorphic markers. An investigation into the genetic diversity of several C. chekiangoleosa populations also suggested that the developed SSR markers had higher levels of polymorphism. This study will provide a reference and high-quality markers for the large-scale development of functional SSR markers and genetic research in Oil-camellia.