TCMPG: an integrative database for traditional Chinese medicine plant genomes

Meng, Fanbo; Tang, Qiang; Chu, Tianzhe; Li, Xianhai; Lin, Yue; Song, Xiaoming; Chen, Wei

doi:10.1093/hr/uhac060

Cited by 21 publications

(8 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The RNAME database was developed based on the python-based Django framework. The user-friendly web page was written in html, CSS and JavaScript, with all data stored and organized in MySQL [52] . An interactive web interface was constructed to allows users to access, visualize, analyze, and obtain required information of RNA modification effectors ( Fig.…”

Section: Resultsmentioning

confidence: 99%

RNAME: A comprehensive database of RNA modification enzymes

Nie

Tang

Liu

et al. 2022

Computational and Structural Biotechnology Journal

Self Cite

View full text Add to dashboard Cite

Section: Resultsmentioning

confidence: 99%

RNAME: A comprehensive database of RNA modification enzymes

Nie

Tang

Liu

et al. 2022

Computational and Structural Biotechnology Journal

Self Cite

View full text Add to dashboard Cite

“…Utilizing high-quality genome sequencing, we investigated the molecular synthesis and efficient accumulation mechanisms of unique metabolites. Medicinal plants of the Lamiaceae family, such as Mentha longifolia, S. miltiorrhiza, Salvia bowleyana, Scutellaria barbata, Salvia splendens, Ocimum basilicum, Origanum majoran a, Origanum vulgare, Pogostemon cablin , and Rosmarinus officinalis have been sequenced ( Meng et al., 2022 ). Among them, S. miltiorrhiza , S. bowleyana , S. barbat , and P. cablin were assembled chromosomes.…”

Section: Discussionmentioning

confidence: 99%

Whole genome and transcriptome reveal flavone accumulation in Scutellaria baicalensis roots

Wang

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Scutellaria baicalensis Georgi is a medicinal plant in the Lamiaceae family that contains high levels of 4’-deoxyflavone and other flavonoids in its roots. Therefore, it has strong potential as a plant resource for researching the biosynthesis of specific flavonoids. In this study, we report on a chromosome-level S. baicalensis genome assembled to nine chromosomes (376.81M) using PacBio, HiSeq XTen, and Hi-C assisted assembly. The assembly ratio was 99.22%, the contig N50 was 1.80 million bases, and the scaffold N50 was 40.57 million bases, with 31896 genes being annotated. Comparative genome analysis revealed that S. baicalensis and Salvia miltiorrhiza belonged to the same branch, and diverged 36.3 million years ago. Other typically correlated species were Boea hygrometrica and Sesamum indicum. We investigated the structural genes involved in flavonoid synthesis in combination with transcriptome sequencing analysis for different tissues (roots, stems, flowers, leaves) of purple, pink, and white flowers. The results revealed that S.baiF6H is involved in the accumulation of baicalein and was significantly increased in both purple roots vs. pink roots and white roots vs. pink roots. S.baiMYB gene family expression pattern analysis and co-expression network analysis revealed that S.baiMYB transcription factors primarily regulated the production of flavonoids in S. baicalensis. S.baiMYB serves as a major factor regulating flavonoid synthesis in the roots, where yeast one-hybrid assays revealed that these transcription factors could bind to the promoter regions of structural genes to control the accumulation of flavonoids. Genome and transcriptome sequencing, co-expression analysis, and yeast one-hybrid experiments provided valuable genetic resources for understanding flavonoid biosynthesis in S. baicalensis. These findings contribute to a better understanding of the accumulation of metabolites in Lamiaceae.

show abstract

“…We used Blastp (E-value <1e-5, identify >50%, score > 200) to identify the homologous genes related to triterpene synthesis in P. tenuifolia and the four legume plants ( A. duranensis , M. truncatula , P. vulgaris , and G. max ). We identified the P450 and UGT gene families in P. tenuifolia based on their HMM profiles (PF00067 and PF00201) using the HmmSearch in the TCMPG [ 80 , 81 ]. Heatmaps of gene expression were drawn using the heatmap function in the seaborn library of python.…”

Section: Methodsmentioning

confidence: 99%

Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis

Meng

Chu

Feng

et al. 2023

Horticulture Research

Self Cite

View full text Add to dashboard Cite

Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental disease. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygalaceae family. We sequenced and assembled this genome by a combination of Illumnina, PacBio HiFi, and Hi-C mapping. The assembly includes 19 pseudochromosomes covering ~92.68% of the assembled genome (~769.27 Mb). There are 36,463 protein-coding genes annotated in this genome. Detailed comparative genome analysis revealed that P. tenuifolia experienced two rounds of whole genome duplication that occurred ~39-44 and ~18-20 million years ago, respectively. Accordingly, we systematically reconstructed ancestral chromosomes of P. tenuifolia and inferred its chromosome evolution trajectories from the common ancestor of core eudicots to the present species. Based on the transcriptomics data, enzyme genes and transcription factors involved in the synthesis of triterpenoid saponin in P. tenuifolia were identified. Further analysis demonstrated that whole genome duplications and tandem duplications play critical roles in the expansion of P450 and UGT gene families, which contributed to the synthesis of triterpenoid saponins. The genome and transcriptome data will not only provide valuable resources for comparative and functional genomic researches on Polygalaceae, but also shed light on the synthesis of triterpenoid saponin.

show abstract

TCMPG: an integrative database for traditional Chinese medicine plant genomes

Cited by 21 publications

References 34 publications

RNAME: A comprehensive database of RNA modification enzymes

RNAME: A comprehensive database of RNA modification enzymes

Whole genome and transcriptome reveal flavone accumulation in Scutellaria baicalensis roots

Genome assembly of Polygala tenuifolia provides insights into its karyotype evolution and triterpenoid saponin biosynthesis

Contact Info

Product

Resources

About