Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology

Catechin promotes the germination of Pistacia chinensis seeds via GA biosynthesis

BACKGROUND AND AIMS

Chinese pistachio (Pistacia chinensis), an important horticultural plant species, holds great ornamental value with beautiful leaves and fruits. Seedling propagation of this tree species is restricted by its erratic seed germination; however, the germination mechanism is ambiguous. The aim of this study was to determine the germination mechanism from a novel perspective based on the multi-omics data.

METHODS

The multi-omics technique combined with hormone content measurement was applied to seed germination of Chinese pistachio.

KEY RESULTS

Due to its great accumulation during seed germination, catechin stood out from the identified metabolites in a broadly targeted metabolomic analysis. Exogenous catechin at 10 mg L-1 significantly improved the germination of Chinese pistachio seeds. An interesting result of hormone analysis was that the improving effect of catechin could be attributed to an increase in gibberellic acid 3 (GA3) content rather than a decrease in abscisic acid (ABA) content before germination. Treatments with paclobutrazol (PAC, a GA biosynthesis inhibitor) and PAC + catechin also showed that the promoting effect of catechin on seed germination depends on GA biosynthesis. Transcriptome analysis and qRT‒PCR further revealed that catechin induced the expression of PcGA20ox5 to activate GA biosynthesis. Several transcription factors were induced by catechin and GA treatments, such as TCP, bZIP and C3H, which may play an important regulatory role in GA biosynthesis in a catechin-mediated way.

CONCLUSIONS

Catechin promotes seed germination via GA biosynthesis in Chinese pistachios. This study proposes a novel mechanism by which catechin promotes seed germination via the GA pathway, which provides new insight into a comprehensive understanding of seed dormancy and germination.

Benzoic Acid, Chlorine Dioxide, and 1-Methylcyclopropene Induce Flavonoid Metabolic Shifts in Postharvest Flowering Chinese Cabbage Revealed by High-Dimensional Analytical Data

Flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) is one of the most popular vegetables in China. However, the loss of the functional ingredients in postharvest flowering Chinese cabbage during storage is still serious, owing to the unclear causes of the metabolic shifts. Herein, benzoic acid, chlorine dioxide, and 1-methylcyclopropene (1-MCP) could maintain the quality of postharvest flowering Chinese cabbage, and 1-MCP showed the best effect. Furthermore, transcript-metabolite profiling of the treatments revealed a transcript-metabolite correlation network of the flavonoid biosynthesis pathways with a range of 3 to 3662 differentially expressed genes (DEGs) and a range of 23 to 37 differentially accumulated metabolites (DAMs). Surprisingly, 1-MCP had the best effect on shelf life among the treatments, although chlorine dioxide could stimulate the expression of four critical differential genes (Bra007142, Bra008792, Bra009358, and Bra027457) involved in delaying flavonoid degradation (hesperetin, chalcone, rutin, baicalein). As a result, our findings will help to improve our understanding of the regulation of flavonoid production in relation to the quality of postharvest flowering Chinese cabbage during storage.

Structural characterization and transcript-metabolite correlation network of immunostimulatory effects of sulfated polysaccharides from green alga Ulva pertusa

Three water-soluble polysaccharides (UPPs 1-3) were obtained from edible green alga Ulva pertusa. The chemico-physical analyses indicated that UPPs 1-3 possessed molecular weights of 376.7 kDa, 57.21 kDa, and 131.13 kDa, with sulfate contents of 26.01 ± 8.13%, 9.86 ± 3.24%, and 13.32 ± 6.56%, respectively, and composed of arabinose, galactose, glucose, xylose, galacturonic acid, glucuronic acid, and mannuronic acid, with different ratios. The in vitro studies revealed that UPP-1 showed significant effects on the proliferation and phagocytic activity of macrophage, release of nitric oxide, and secretion of cytokines (TNF-α and IL-6). The transcript-metabolite analysis of UPP-1 treated macrophage revealed 4747 differential genes (2416 up-regulated and 2331 down-regulated) and 94 differential metabolites (77 up-regulated and 17 down-regulated) that significantly co-mapped a transcript-metabolite correlation network of biosynthesis of amino acids, glycerophospholipid metabolism, and carbon metabolism. Thus, these findings provide a valuable foundation for the potential application of U. pertusa polysaccharides.

Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis

BACKGROUND

Leaves of the medicinal plant Ampelopsis grossedentata, which is commonly known as vine tea, are used widely in the traditional Chinese beverage in southwest China. The leaves contain a large amount of dihydromyricetin, a compound with various biological activities. However, the transcript profiles involved in its biosynthetic pathway in this plant are unknown.

RESULTS

We conducted a transcriptome analysis of both young and old leaves of the vine tea plant using Illumina sequencing. Of the transcriptome datasets, a total of 52.47 million and 47.25 million clean reads were obtained from young and old leaves, respectively. Among 471,658 transcripts and 177,422 genes generated, 7768 differentially expressed genes were identified in leaves at these two stages of development. The phenylpropanoid biosynthetic pathway of vine tea was investigated according to the transcriptome profiling analysis. Most of the genes encoding phenylpropanoid biosynthesis enzymes were identified and found to be differentially expressed in different tissues and leaf stages of vine tea and also greatly contributed to the biosynthesis of dihydromyricetin in vine tea.

CONCLUSIONS

To the best of our knowledge, this is the first formal study to explore the transcriptome of A. grossedentata. The study provides an insight into the expression patterns and differential distribution of genes related to dihydromyricetin biosynthesis in vine tea. The information may pave the way to metabolically engineering plants with higher flavonoid content.

Alternative Splicing of Key Genes in LOX Pathway Involves Biosynthesis of Volatile Fatty Acid Derivatives in Tea Plant (Camellia sinensis)

Volatile fatty acid derivatives (VFADs) produced in tea plants (Camellia sinensis) not only have been shown to function as defense compounds but also impart a "fresh green" odor to green tea products; however, little is known about alternative splicing (AS) of genes in regulating the production of VFADs in plants. In this study, the contents of VFADs and corresponding transcriptome profiles were obtained in five different months (April, June, August, September, and October). Correlation analysis identified seven unique transcripts of enzyme-coding genes (CsLOX2, CsLOX4, CsADH4, CsADH8, and CsADH10), which are responsible for regulating VFAD biosynthesis; four AS transcripts of these genes (CsLOX2, CsLOX4, CsADH4, and CsADH8) were validated by RT-PCR. By employing the gene-specific antisense oligodeoxynucleotide-mediated reduction method, we found the expression levels of alternatively spliced transcripts of CsLOX4-iso1, CsLOX4-iso2, and CsADH4-iso3 were lower, and the contents of cis-3-hexenol were correspondingly reduced in the leaves of tea plant; this result suggested that the AS play important roles in regulating biosynthesis of VFADs in C. sinensis. Our results provide new insights into the important contribution of AS events in regulating the VFAD biosynthesis in tea plant.

Metabolome and Transcriptome Sequencing Analysis Reveals Anthocyanin Metabolism in Pink Flowers of Anthocyanin-Rich Tea (Camellia sinensis)

Almost all flowers of the tea plant (Camellia sinensis) are white, which has caused few researchers to pay attention to anthocyanin accumulation and color changing in tea flowers. A new purple-leaf cultivar, Baitang purple tea (BTP) was discovered in the Baitang Mountains of Guangdong, whose flowers are naturally pink, and can provide an opportunity to understand anthocyanin metabolic networks and flower color development in tea flowers. In the present study, twelve anthocyanin components were identified in the pink tea flowers, namely cyanidin O-syringic acid, petunidin 3-O-glucoside, pelargonidin 3-O-beta-d-glucoside, which marks the first time these compounds have been found in the tea flowers. The presence of these anthocyanins seem most likely to be the reason for the pink coloration of the flowers. Twenty-one differentially expressed genes (DEGs) involved in anthocyanin pathway were identified using KEGG pathway functional enrichment, and ten of these DEG’s screened using venn and KEGG functional enrichment analysis during five subsequent stages of flower development. By comparing DEGs and their expression levels across multiple flower development stages, we found that anthocyanin biosynthesis and accumulation in BTP flowers mainly occurred between the third and fourth stages (BTP3 to BTP4). Particularly, during the period of peak anthocyanin synthesis 17 structural genes were upregulated, and four structural genes were downregulated only. Ultimately, eight critical genes were identified using weighted gene co-expression network analysis (WGCNA), which were found to have direct impact on biosynthesis and accumulation of three flavonoid compounds, namely cyanidin 3-O-glucoside, petunidin 3-O-glucoside and epicatechin gallate. These results provide useful information about the molecular mechanisms of coloration in rare pink tea flower of anthocyanin-rich tea, enriching the gene resource and guiding further research on anthocyanin accumulation in purple tea.

Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)

Flavonoids, theanine and caffeine are the main secondary metabolites of the tea plant (Camellia sinensis), which account for the tea's unique flavor quality and health benefits. The biosynthesis pathways of these metabolites have been extensively studied at the transcriptional level, but the regulatory mechanisms are still unclear. In this study, to explore the transcriptome diversity and complexity of tea plant, PacBio Iso-Seq and RNA-seq analysis were combined to obtain full-length transcripts and to profile the changes in gene expression during the leaf development. A total of 1,388,066 reads of insert (ROI) were generated with an average length of 1,762 bp, and more than 54% (755,716) of the ROIs were full-length non-chimeric (FLNC) reads. The Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness was 92.7%. A total of 93,883 non-redundant transcripts were obtained, and 87,395 (93.1%) were new alternatively spliced isoforms. Meanwhile, 7,650 differential expression transcripts (DETs) were identified. A total of 28,980 alternative splicing (AS) events were predicted, including 1,297 differential AS (DAS) events. The transcript isoforms of the key genes involved in the flavonoid, theanine and caffeine biosynthesis pathways were characterized. Additionally, 5,777 fusion transcripts and 9,052 long non-coding RNAs (lncRNAs) were also predicted. Our results revealed that AS potentially plays a crucial role in the regulation of the secondary metabolism of the tea plant. These findings enhanced our understanding of the complexity of the secondary metabolic regulation of tea plants and provided a basis for the subsequent exploration of the regulatory mechanisms of flavonoid, theanine and caffeine biosynthesis in tea plants.

Comparative transcriptome analysis of genes involved in anthocyanin synthesis in blueberry

Blueberry (Vaccinium, family Ericaceae) is well known for its strong antioxidant properties and abundant active ingredients including anthocyanins, flavonols, and proanthocyanidins. In this study, variations in anthocyanin and phenolic compounds content in Bluecrop and Northblue blueberry cultivar fruits were studied, and comparative transcriptome analysis was performed to analyze differences in the molecular mechanisms of anthocyanin biosynthesis. A total of 13 799 unique genes were identified by differential expression analysis, and further subjected to GO classification and pathway enrichment. Nine differentially expressed genes (DEGs), including CHI, DFR, F3'H, FLS, CHS, OMT, UGT, ANS and F3H, were selected to validate the differential expression data using quantitative real-time PCR. The obtained qRT-PCR expression results were consistent with the RNA-Seq results. The expression levels of 9 candidate genes involved in flavonoid biosynthesis and metabolism were concurrent with the anthocyanin content. The developmental stage appeared to affect the expression of genes related to flavonoid biosynthesis to a greater extent than the tissue or cultivar type. This study provides an abundant data resource that will further our understanding of the molecular mechanisms of anthocyanin biosynthesis in blueberries.

Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses

Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants.