Trends in herbgenomics

Xin, Tianyi; Pu, Xiangdong; Gao, Ranran; Xu, Zhichao; Song, Jingyuan

doi:10.1007/s11427-018-9352-7

Cited by 48 publications

(23 citation statements)

References 169 publications

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“…With the rapid development of next-generation sequencing technology, whole-genome information has been obtained for many medicinal plants. Herbgenomics is a new field of study that investigates the genetics and regulatory mechanisms of traditional Chinese herbal medicines via genomics, which clarifies the mechanisms of action of traditional Chinese medicines and facilitates molecular breeding from the perspective of the genome (Chen and Song, 2016; Xin et al, 2018). Herbgenomics mainly involves analysis of medicinal plant genomes, transcriptomes, proteomes, metabolomes, and so on.…”

Section: Introductionmentioning

confidence: 99%

Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum

Zhang

Zheng

et al. 2019

Front. Plant Sci.

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Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue, and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.

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Section: Introductionmentioning

confidence: 99%

Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum

Zhang

Zheng

et al. 2019

Front. Plant Sci.

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“…The Salvia miltiorrhiza genome from the Lamiaceae family provides useful information associated with secondary metabolism for the rapid functional identification of biosynthetic and regulatory genes [18−23]. In contrast, the genomes of the Scutellara genus remains unclear, and the reliance on transcriptome data from short-read sequencing has restricted gene discovery and analyses of genome evolution, including studies of gene family expansion and contraction, the evolution of biosynthetic genes, and identification of regulatory elements [24].…”

Section: Introductionmentioning

confidence: 99%

Comparative Genome Analysis ofScutellaria baicalensisandScutellaria barbataReveals the Evolution of Active Flavonoid Biosynthesis

Gao

et al. 2020

Preprint

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39 Scutellaria baicalensis and Scutellaria barbata, common medicinal plants of the 40 Lamiaceae family, produce specific flavonoid compounds with antioxidant and 41 antitumor activities, including baicalein, scutellarein, norwogonin, wogonin, and their 42 glycosides. Here, we reported two chromosome-level genome assemblies of S. 43 baicalensis and S. barbata with significant quantitative chromosomal variation (2n = 44 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred 45 far earlier than previously reported, and a whole-genome duplication event was 46 identified. The insertion of long terminal repeat elements after speciation might be 47 responsible for the observed chromosomal expansion and rearrangement. The 48 comparative genome analysis of congeneric species elucidated the species-specific 49 evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific 50 tandem duplication of the phenylalanine ammonia lyase (PAL) and chalcone synthase 51 (CHS) genes, and the S. barbata-specific duplication of 4-CoA ligase (4CL) genes. In 52 addition, the paralogous duplication, collinearity, and expression diversity of CYP82D 53 subfamily members revealed the functional divergence of flavone hydroxylase genes 54 between S. baicalensis and S. barbata. These Scutellaria genomes highlight the 55 common and species-specific evolution of flavone biosynthetic genes, promoting the 56 development of molecular breeding and the study of the biosynthesis and regulation of 57 bioactive compounds.58 59 KEYWORDS: Scutellaria; comparative genome; flavonoid biosynthesis; tandem 60 duplication; species-specific evolution 61 62 63 65 proanthocyanidins, and isoflavones, play important functions in plants, such as flower 66 pigmentation, UV protection, and symbiotic nitrogen fixation [1−3]. Flavonoid 67 metabolites also have biological and pharmacological activities in human health, 68 including antibacterial and antioxidant functions, and the treatment of cancer, 69 inflammatory, and cardiovascular diseases [3]. The genus Scutellaria, belong to the 70 Lamiaceae family, comprises common herbal plants enriched by bioactive flavonoids, 71 and approximately 300 to 360 Scutellaria species have been documented as having the 72 characteristic flower form of upper and lower lips [4,5]. Only two Scutellaria species, 73 Scutellaria baicalensis and Scutellaria barbata, are recorded in the Chinese 74 pharmacopoeia, and the roots of S. baicalensis and dried herbs of S. barbata are the 75 basis of the Chinese medicines Huang Qin and Ban Zhi Lian, respectively, which have 76 been well known heat-clearing and detoxifying herbs for thousands of years [6]. The 77 main biologically active compounds in Scutellaria are derivatives of chrysin and 78 apigenin, such as baicalein, scutellarein, wogonin, and their glycosides (baicalin, 79 scutellarin, and wogonoside) [7−10]. Baicalin has been confirmed to activate carnitine 80 palmitoyltransferase 1 in the treatment of diet-induced obesity and hepatic st...

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“…Cassia seed is the dried ripe seed of the leguminous plant Cassia obtusifolia L. or Cassia tora L. (8). It was first recorded in 'Shen Nong's Herbal Classic' (9). The seed displays extensive pharmacological actions, for example, modern pharmacological research has reported that the cassia seed possesses antibacterial activity (10,11).…”

Section: Introductionmentioning

confidence: 99%

Metabolite identification of gut microflora‑cassia seed interactions using UPLC‑QTOF/MS

et al. 2020

Exp Ther Med

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Cassia seed is the dried ripe seed of Cassia obtusifolia L. or Cassia tora L., which is widely used as a food or traditional Chinese medicine. The aim of the present study was to detect the components and metabolites in the culture of human or rat intestinal microflora suspension with the water decoction of cassia seed in vitro, using an ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry system equipped with a negative ion scan mode. Initially, ellagic acid was identified in the cassia seed decoction. Subsequently, six different metabolites, including urolithin (uro)-A, uro-B, uro-D, uro-M6, uro-M7 and uro-B-glucuronide (glur), were detected after co-culture of the cassia seed decoction with intestinal microflora, but not in the cassia seed decoction alone. Uro-M6, uro-M7, uro-A and uro-B were common metabolites in the culture of human or rat intestinal microflora suspension with the water decoction of cassia seed. However, uro-D was only detected in the culture of rat intestinal microflora suspension with the water decoction of cassia seed, and uro-B-glur was only detected in the culture of human intestinal microflora with the water decoction of cassia seed. The uro and intermediate metabolites were produced by ellagic acid in the cassia seed decoction under the action of the intestinal microflora. The production of metabolites might be related to the abundance and diversity of the intestinal microflora in humans and rats. The present study provided rationale for further pharmacological and clinical studies on the mechanisms of action of cassia seeds.

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Trends in herbgenomics

Cited by 48 publications

References 169 publications

Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum

Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatum

Comparative Genome Analysis ofScutellaria baicalensisandScutellaria barbataReveals the Evolution of Active Flavonoid Biosynthesis

Metabolite identification of gut microflora‑cassia seed interactions using UPLC‑QTOF/MS

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