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

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About: A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome
Creator	Yang, Qiao Huang, Li Hu, Quanjun Kang, Minghui Li, Zaiyun Liu, Jianquan Ma, Tao Wu, Haolin
Source	Medline; PMC
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.
has issue date	2020-02-01(xsd:dateTime)
bibo:doi	10.1038/s41438-020-0240-5
bibo:pmid	32025321
has license	cc-by
sha1sum (hex)	6d756b7df1778be58daa0e30caefc968807d6a80
schema:url	https://doi.org/10.1038/s41438-020-0240-5
resource representing a document's title	A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine: An Isatis genome
has PubMed Central identifier	PMC6994597
has PubMed identifier	32025321
schema:publication	Hortic Res
resource representing a document's body	covid:6d756b7df1778be58daa0e30caefc968807d6a80#body_text
is schema:about of	named entity 'biosynthesis' named entity 'identified' named entity 'influenza' named entity 'revealed' named entity 'species' named entity 'scaffold' named entity 'Radix' named entity 'candidate' named entity 'isolated' named entity 'compounds' named entity 'high-throughput' named entity 'phenylpropanoids' named entity 'GENOME SEQUENCING' named entity 'EXPLAINED' named entity 'HORTICULTURE' named entity 'ISOLATED' named entity 'MOLECULE' named entity 'TERPENOIDS' named entity 'ACTIVITIES' named entity 'DRIED' named entity 'VIRAL PNEUMONIA' named entity 'HIGH' named entity 'METABOLITE' named entity 'IDENTIFYING' named entity 'FOUND' named entity 'DROVE' named entity 'ADDITION' named entity 'GENOME ASSEMBLY' named entity 'EXPANDED ' named entity 'VIRUSES' named entity 'BASED' named entity 'TRADITIONAL CHINESE MEDICINE' named entity 'TOTAL' named entity 'EXCELLENT' named entity 'DUE TO' named entity 'REVEALED' named entity 'FOLIUM' named entity 'PREVIOUS' named entity 'CLASSES' named entity 'BIOSYNTHESIS' named entity 'CURING DISEASES' named entity 'ISATIS INDIGOTICA' named entity 'RESEARCH' named entity 'CHROMOSOME' named entity 'IMPORTANT' named entity 'MEDICINAL PLANT' named entity 'ISATIS' named entity 'SCALE' named entity 'GENOME' named entity 'USED' named entity 'ANTIVIRAL' named entity 'GENE FAMILIES' named entity 'DISEASES CAUSED BY BACTERIA' named entity 'USING' named entity 'DUPLICATIONS' named entity 'IDENTIFIED' named entity 'TECHNIQUES' named entity 'HOMOLOG' named entity 'READS' named entity 'PHENYLPROPANOIDS' named entity 'SPECIES' named entity 'HAVE' named entity 'SCALE' named entity 'CHINA' named entity 'HERE' named entity 'COMPONENTS' named entity 'ITS' named entity 'CHROMOSOME CONFORMATION CAPTURE' named entity 'CODING' named entity 'THESE' named entity 'RELATED' named entity 'REAL-TIME' named entity 'CHROMOSOME' named entity 'INDOLES'

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