Transcriptional analysis of Rhazya stricta in response to jasmonic acid

BACKGROUND: Jasmonic acid (JA) is a signal transducer molecule that plays an important role in plant development and stress response; it can also efficiently stimulate secondary metabolism in plant cells. RESULTS: RNA-Seq technology was applied to identify differentially expressed genes and study the time course of gene expression in Rhazya stricta in response to JA. Of more than 288 million total reads, approximately 27% were mapped to genes in the reference genome. Genes involved during the secondary metabolite pathways were up- or downregulated when treated with JA in R. stricta. Functional annotation and pathway analysis of all up- and downregulated genes identified many biological processes and molecular functions. Jasmonic acid biosynthetic, cell wall organization, and chlorophyll metabolic processes were upregulated at days 2, 6, and 12, respectively. Similarly, the molecular functions of calcium-transporting ATPase activity, ADP binding, and protein kinase activity were also upregulated at days 2, 6, and 12, respectively. Time-dependent transcriptional gene expression analysis showed that JA can induce signaling in the phenylpropanoid and aromatic acid pathways. These pathways are responsible for the production of secondary metabolites, which are essential for the development and environmental defense mechanism of R. stricta during stress conditions. CONCLUSIONS: Our results suggested that genes involved in flavonoid biosynthesis and aromatic acid synthesis pathways were upregulated during JA stress. However, monoterpenoid indole alkaloid (MIA) was unaffected by JA treatment. Hence, we can postulate that JA plays an important role in R. stricta during plant development and environmental stress conditions.

Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis / 基因组蛋白质组与生物信息学报·英文版

Scutellaria baicalensis (S. baicalensis) and Scutellaria barbata (S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensis and S. barbata with quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred far earlier than previously reported, and a whole-genome duplication (WGD) event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. Comparative genome analysis of the congeneric species revealed the species-specific evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of genes encoding phenylalanine ammonia lyase and chalcone synthase, and the S. barbata-specific duplication of genes encoding 4-CoA ligase. In addition, the paralogous duplication, colinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensis and S. barbata. Analyzing these Scutellaria genomes reveals the common and species-specific evolution of flavone biosynthetic genes. Thus, these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.

Linking the platelet antiaggregation effect of different strawberries species with antioxidants: metabolomic and transcript profiling of polyphenols / Asociando el efecto de antiagregación plaquetaria de distintas especies de frutillas con antioxidantes: perfil metabolómico y transcriptómico de polifenoles

A comparative study of antioxidant properties, platelet antiaggregation activity and transcriptional analysis of flavonoid biosynthesis genes were performed in Fragaria x ananassa, F. vesca and F. chiloensis subsp chiloensis f. chiloensis and f. patagonica. Furthermore, differences in flavonoid content were found by UHPLC-MS. The highest free radical scavenging activity by DPPH assay was observed in F. chiloensis f. chiloensis, meanwhile, F. vesca presented the highest antioxidant capacity by FRAP. Biosynthetic flavonoids- related transcripts were higher abundant in F. x ananassa and lower in F. vesca. Additionally, all strawberry extracts showed antiaggregant effect (1 mg mL-1), but F. vesca and F. chiloensis subsp. chiloensis f. patagonica were still active at lower concentration. This study suggests that platelet antiaggregation effect of different strawberries could be due to isoflavones and flavonoids precursors in addition to anthocyanins. Results could usefully to take decisions in future breeding programs to improve the content of healthy compounds in strawberry fruits.

Se realizó un estudio comparativo de propiedades antioxidantes, actividad de antiagregacion plaquetaria, análisis transcripcional de genes de biosíntesis de flavonoides y contenido de estos en Fragaria x ananassa, F. vesca and F. chiloensis subsp chiloensis f. chiloensis and f. patagonica. La mayor actividad removedora de radicales libres por DPPH se observó en F. chiloensis f. chiloensis, mientras F. vesca presentó la mayor capacidad antioxidante mediante FRAP. Transcritos relacionados con biosíntesis de flavonoides fueron mas abundantes en F. x ananassa y menores en F. vesca. Adicionalmente, todos los extractos de frutillas mostraron efectos antiagregante (1 mg mL-1), pero F. vesca and F. chiloensis subsp. chiloensis f. patagonica fueron activos a concentraciones menores. Este estudio sugiere que efectos de antiagregación plaquetaria en distintas frutillas podría deberse a isoflavonas y precursores de flavonoides además de antocianinas. Los resultados podrían ser útiles en programas de mejoramiento genético para mejorar el contenido de compuestos saludables en frutilla.

Analysis of transcriptome sequencing and qRT-PCR analysis of related genes of flavonoid biosynthesis from Eucommia ulmoides calli / 中草药

Objective To analyse the transcriptome sequencing results of Eucommia ulmoides calli under light and dark culture condition, and verify the expression level of the related genes of flavonoid biosynthesis from transcriptome sequencing results. Methods The transcriptome high-throughput sequencing of E. ulmoides calli was performed by using the Illumina HiSeqTM 2500 sequencing platform, and de novo assembly of the transcriptome sequencing results was finished by Trinity software. The sequencing results of Unigenes were compared with the databases of NR, Swiss-Prot, GO, COG, KOG, KEGG and Pfam by BLAST software. The gene expression abundance was estimated by FPKM value. qRT-PCR was used to verify the expression level of the related genes of flavonoid biosynthesis. Results About 13.00 Giga base pairs (Gbp) clean data (more than 6.02 Gbp, respectively) were obtained, and de novo assembly generated 62 030 Unigenes with an average length of 736.40 bp. A total of 25 167 Unigenes were annotated to Nr. Totally 4 794 Unigenes and their associated enzymes (enzyme commission numbers) were annotated to 82 KEGG pathway. There were 1 986 genes identified as significantly and differentially expressed genes between the two calli under light and dark culture. Among them, 1 139 (57.35%) were up-regulated and 847 (42.65%) were down-regulated in the calli under light culture. Metabolic pathway analysis revealed that seven Unigenes were predicted to be responsible for the flavonoid biosynthesis, six Unigenes of which were up-regulated in the calli under light culture, encoding chalcone isomerase (EC 5.5.1.6), chalcome synthase (EC 2.3.1.74), flavonoid 3’-monooxygenase (EC1.14.13.21), trans-cinnamate 4-monooxygenase (EC 1.14.13.11), Flavonol synthase (EC 1.14.11.23), shikimate-O-hydroxycinnamoyl transferase (EC 2.3.1.133). One Unigene was down-regulated in the calli under light culture, which encoded leucocyanidin oxygenase (EC 1.14.11.19). qRT-PCR analysis showed that the expression of the seven genes related with flavonoid biosynthesis was coincident with the transcriptome high-throughput sequencing results. Conclusion The white light (12 000 lx, 16 h light and 8 h dark) could improve the production capacity of some metabolic intermediate of flavonoid biosynthesis pathway of E. ulmoides calli.