Transcriptomics and Metabolomics Analyses Reveal Defensive Responses and Flavonoid Biosynthesis of Dracaena cochinchinensis (Lour.) S. C. Chen under Wound Stress in Natural Conditions.

Dracaena cochinchinensis has special defensive reactions against wound stress. Under wound stress, D. cochinchinensis generates a resin that is an important medicine known as dragon's blood. However, the molecular mechanism underlying the defensive reactions is unclear. Metabolomics and transcriptomics analyses were performed on stems of D. cochinchinensis at different timepoints from the short term to the long term after wounding. According to the 378 identified compounds, wound-induced secondary metabolic processes exhibited three-phase characteristics: short term (0-5 days), middle term (10 days-3 months), and long term (6-17 months). The wound-induced transcriptome profile exhibited characteristics of four stages: within 24 h, 1-5 days, 10-30 days, and long term. The metabolic regulation in response to wound stress mainly involved the TCA cycle, glycolysis, starch and sucrose metabolism, phenylalanine biosynthesis, and flavonoid biosynthesis, along with some signal transduction pathways, which were all well connected. Flavonoid biosynthesis and modification were the main reactions against wound stress, mainly comprising 109 flavonoid metabolites and 93 wound-induced genes. A group of 21 genes encoding CHS, CHI, DFR, PPO, OMT, LAR, GST, and MYBs were closely related to loureirin B and loureirin C. Wound-induced responses at the metabolome and transcriptome level exhibited phase characteristics. Complex responses containing primary metabolism and flavonoid biosynthesis are involved in the defense mechanism against wound stress in natural conditions, and flavonoid biosynthesis and modification are the main strategies of D. cochinchinensis in the long-term responses to wound stress.

Screening and validation of reference genes in Dracaena cochinchinensis using quantitative real-time PCR.

Dragon's blood, the red resin derived from the wounded Dracaena, is a precious traditional medicine used by different culture. Dracaena cochinchinensis is one of the main species of Dracaena, and is the endangered medicinal plants in China. The vulnerable status severely limits the medicinal value and wide application of dragon's blood. Therefore, it's essential to analyze the mechanisms that form dragon's blood in order to increase artificial production. To clarify the mechanisms forming dragon's blood, understanding gene expression in the flavonoid biosynthesis pathway is the foundation. However, reference genes of D. cochinchinensis haven't been analyzed. In this study, expression profiles of seven commonly used housekeeping genes (Actin, α-EF, UBC, ß-tubulin, 18S, GAPDH, His) were evaluated by using quantitative real-time PCR combined with the algorithms geNorm, NormFinder, BestKeeper, and RefFinder. On the basis of overall stability ranking, the best reference genes were the combinations ß-tubulin +UBC for wounded stems and α-EF +18S + Actin for different organs. Reliability of the recommended reference genes was validated by normalizing relative expression of two key enzyme genes PAL1 and CHI1 in the flavonoid biosynthesis pathway. The results provide a foundation to study gene expression in future research on D. cochinchinensis or other Dracaena.

The LOB domain protein, a novel transcription factor with multiple functions: A review.

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) protein, named for its LATERAL ORGAN BOUNDARIES (LOB) domain, is a member of a class of specific transcription factors commonly found in plants and is absent from all other groups of organisms. LBD TFs have been systematically identified in about 35 plant species and are involved in regulating various aspects of plant growth and development. However, research on the signaling network and regulatory functions of LBD TFs is insufficient, and only a few members have been studied. Moreover, a comprehensive review of these existing studies is lacking. In this review, the structure, regulatory mechanism and function of LBD TFs in recent years were reviewed in order to better understand the role of LBD TFs in plant growth and development, and to provide a new perspective for the follow-up study of LBD TFs.

Identification and characterization of novel sesquiterpene synthases TPS9 and TPS12 from Aquilaria sinensis.

Sesquiterpenes are characteristic components and important quality criterions for agarwood. Although sesquiterpenes are well-known to be biosynthesized by sesquiterpene synthases (TPSs), to date, only a few TPS genes involved in agarwood formation have been reported. Here, two new TPS genes, namely, TPS9 and TPS12, were isolated from Aquilaria sinensis (Lour.) Gilg, and their functions were examined in Escherichia coli BL21(DE3), with farnesyl pyrophosphate (FPP) and geranyl pyrophosphate (GPP) as the substrate of the corresponding enzyme activities. They were both identified as a multiproduct enzymes. After incubation with FPP, TPS9 liberated ß-farnesene and cis-sesquisabinene hydrate as main products, with cedrol and another unidentified sesquiterpene as minor products. TPS12 catalyzes the formation of ß-farnesene, nerolidol, γ-eudesmol, and hinesol. After incubation with GPP, TPS9 generated citronellol and geraniol as main products, with seven minor products. TPS12 converted GPP into four monoterpenes, with citral as the main product, and three minor products. Both TPS9 and TPS12 showed much higher expression in the two major tissues emitting floral volatiles: flowers and agarwood. Further, RT-PCR analysis showed TPS9 and TPS12 are typical genes mainly expressed during later stages of stress response, which is better known than that of chromone derivatives. This study will advance our understanding of agarwood formation and provide a solid theoretical foundation for clarifying its mechanism in A. sinensis.

A chromosome-level genome assembly for Dracaena cochinchinensis reveals the molecular basis of its longevity and formation of dragon's blood.

Dracaena, a remarkably long-lived and slowly maturing species of plant, is world famous for its ability to produce dragon's blood, a precious traditional medicine used by different cultures since ancient times. However, there is no detailed and high-quality genome available for this species at present; thus, the molecular mechanisms that underlie its important traits are largely unknown. These factors seriously limit the protection and regeneration of this rare and endangered plant resource. Here, we sequenced and assembled the genome of Dracaena cochinchinensis at the chromosome level. The D. cochinchinensis genome covers 1.21 Gb with a scaffold N50 of 50.06 Mb and encodes 31 619 predicted protein-coding genes. Analysis showed that D. cochinchinensis has undergone two whole-genome duplications and two bursts of long terminal repeat insertions. The expansion of two gene classes, cis-zeatin O-glucosyltransferase and small auxin upregulated RNA, were found to account for its longevity and slow growth. Two transcription factors (bHLH and MYB) were found to be core regulators of the flavonoid biosynthesis pathway, and reactive oxygen species were identified as the specific signaling molecules responsible for the injury-induced formation of dragon's blood. Our study provides high-quality genomic information relating to D. cochinchinensis and significant insight into the molecular mechanisms responsible for its longevity and formation of dragon's blood. These findings will facilitate resource protection and sustainable utilization of Dracaena.