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A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome.

ABSTRACT: Isatis indigotica (2n?=?14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the biosynthesis of these active compounds in this medicinal plant. Here, we report a high-quality chromosome-scale genome assembly of I. indigotica with a total size of 293.88?Mb and scaffold N50?=?36.16?Mb using single-molecule real-time long reads and high-throughput chromosome conformation capture techniques. We annotated 30,323 high-confidence protein-coding genes. Based on homolog searching and functional annotations, we identified many candidate genes involved in the biosynthesis of main active components such as indoles, terpenoids, and phenylpropanoids. In addition, we found that some key enzyme-coding gene families related to the biosynthesis of these components were expanded due to tandem duplications, which likely drove the production of these major active compounds and explained why I. indigotica has excellent antibacterial and antiviral activities. Our results highlighted the importance of genome sequencing in identifying candidate genes for metabolite synthesis in medicinal plants.

SUBMITTER: Kang M

PROVIDER: S-EPMC6994597 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome.

Kang Minghui M Wu Haolin H Yang Qiao Q Huang Li L Hu Quanjun Q Ma Tao T Li Zaiyun Z Liu Jianquan J

Horticulture research 20200201

Isatis indigotica (2n = 14) is an important medicinal plant in China. Its dried leaves and roots (called Isatidis Folium and Isatidis Radix, respectively) are broadly used in traditional Chinese medicine for curing diseases caused by bacteria and viruses such as influenza and viral pneumonia. Various classes of compounds isolated from this species have been identified as effective ingredients. Previous studies based on transcriptomes revealed only a few candidate genes for the bios ...[more]

PMID: 32025321

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Project description:BackgroundOaxaca is one of the most diverse states in Mexico from biological and cultural points of view. Different ethnic groups living there maintain deep and ancestral traditional knowledge of medicinal plants as well as traditional practices and beliefs about diseases/illnesses and cures. Previous ethnobotanical research in this state has helped document this knowledge, but with the addition of more studies, more records appear. We updated the inventory of medicinal knowledge between the different ethnic groups that inhabit the Oaxacan territory.MethodsA database was constructed from two sources: (1) original data from a 3-year project in 84 municipalities of Oaxaca inhabited by eight ethnic groups and (2) different electronic databases.ResultsRecords of 1032 medicinal plants were obtained; 164 families were registered, with Asteraceae, Fabaceae, and Rubiaceae being the most commonly used. A total of 770 species were reported in 14 vegetation types; the most important species came from temperate forests. Only 144 species corresponded to introduced species, and 272 were listed in a risk category. Illnesses of the digestive and genitourinary systems as well as culture-bound syndromes were treated with high numbers of medicinal plants. The Mestizo, Mixe, Mixtec, and Zapotec ethnic groups exhibited the greatest number of recorded medicinal plants. The 17 species that were used among almost all ethnic groups in Oaxaca were also used to cure the highest number of diseases.DiscussionInventories of medicinal plants confirm the persistence of traditional knowledge and reflect the need to recognize and respect this cosmovision. Many species are gathered in wild environments. The most important illnesses or diseases recorded in the present inventory are also mentioned in different studies, suggesting that they are common health problems in the rural communities of Mexico.ConclusionsMedicinal plants are essential for ethnic groups in Oaxaca. It is necessary to recognize and understand the complex ancestral processes involved in the human-nature interaction and the role of these processes in the conservation of biodiversity and in the survivorship of ethnic groups that have persisted for centuries. Finally, this study serves as a wake-up call to respect those worldviews.

Project description:Parkinson's disease (PD) is a neurodegenerative disorder characterized by a loss of dopaminergic neurons in the substantia nigra pars compacta and the presence in surviving neurons of Lewy body inclusions enriched with aggregated forms of the presynaptic protein ?-synuclein (aSyn). Although current therapies provide temporary symptomatic relief, they do not slow the underlying neurodegeneration in the midbrain. In this study, we analyzed contemporary herbal medicinal practices used by members of the Lumbee tribe to treat PD-related symptoms, in an effort to identify safe and effective herbal medicines to treat PD.The aims of this study were to (i) document medicinal plants used by Lumbee Indians to treat PD and PD-related symptoms, and (ii) characterize a subset of plant candidates in terms of their ability to alleviate neurotoxicity elicited by PD-related insults and their potential mechanisms of neuroprotection.Interviews of Lumbee healers and local people were carried out in Pembroke, North Carolina, and in surrounding towns. Plant samples were collected and prepared as water extracts for subsequent analysis. Extracts were characterized in terms of their ability to induce activation of the nuclear factor E2-related factor 2 (Nrf2) antioxidant response in cortical astrocytes. An extract prepared from Sambucus caerulea flowers (elderflower extract) was further examined for the ability to induce Nrf2-mediated transcription in induced pluripotent stem cell (iPSC)-derived astrocytes and primary midbrain cultures, to ameliorate mitochondrial dysfunction, and to alleviate rotenone- or aSyn-mediated neurotoxicity.The ethnopharmacological interviews resulted in the documentation of 32 medicinal plants used to treat PD-related symptoms and 40 plants used to treat other disorders. A polyphenol-rich extract prepared from elderflower activated the Nrf2-mediated antioxidant response in cortical astrocytes, iPSC-derived astrocytes, and primary midbrain cultures, apparently via the inhibition of Nrf2 degradation mediated by the ubiquitin proteasome system. Furthermore, the elderflower extract rescued mitochondrial functional deficits in a neuronal cell line and alleviated neurotoxicity elicited by rotenone and aSyn in primary midbrain cultures.These results highlight potential therapeutic benefits of botanical extracts used in traditional Lumbee medicine, and they provide insight into mechanisms by which an elderflower extract could suppress neurotoxicity elicited by environmental and genetic PD-related insults.

Dataset Information

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome.

Publications

A chromosome-scale genome assembly of <i>Isatis indigotica</i>, an important medicinal plant used in traditional Chinese medicine: An <i>Isatis</i> genome.

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