ArticleHorticulture research2021
The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis.
Article in Horticulture research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Comprehensive analysis of synonymous codon usage bias and evolutionary dynamics in the chloroplast genomes of eight Coptis species.Functional & integrative genomics · 2026Article
- Chromosome-scale assembly of the eliteHorticulture research · 2026Article
- The Nigella damascena genome provides insights into transposable element-driven genomic gigantism and trait evolution.Nature communications · 2026Article
- Genome-Wide Identification of the GRAS Transcription Factor Family inInternational journal of molecular sciences · 2026Article
- Integrated Transcriptome and Metabolome Analysis Reveals Differential Berberine Biosynthesis in Leaves and Stems ofCurrent issues in molecular biology · 2026Article
- Integrated Metabolomics and Transcriptomics Analysis Reveals the Biosynthetic Mechanism of Isoquinoline Alkaloids in Different Tissues ofCurrent issues in molecular biology · 2026Article
- Genotyping-by-Sequencing Reveals Low Genetic Diversity and Pronounced Geographic Structuring in the Endangered Medicinal PlantPlants (Basel, Switzerland) · 2026Article
- Genome-Wide Identification and Analysis of bZIP Transcription Factors inInternational journal of molecular sciences · 2025Article
- Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (International journal of molecular sciences · 2025Article
- Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).The Plant journal : for cell and molecular biology · 2025Article
- Genome-Wide Identification and Functional Analysis of the Norcoclaurine Synthase Gene Family inInternational journal of molecular sciences · 2025Article
- Genome-Wide Screening of the MYB Genes inGenes · 2025Article
- Chromosome-scale genome assembly and annotation of Huzhang (Reynoutria japonica).Scientific data · 2025Article
- A long road ahead to reliable and complete medicinal plant genomes.Nature communications · 2025Review
- Lineage-Specific CYP80 Expansion and Benzylisoquinoline Alkaloid Diversity in Early-Diverging Eudicots.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- A cornucopia of diversity-Ranunculales as a model lineage.Journal of experimental botany · 2024Review
- Whole-genome sequencing in medicinal plants: current progress and prospect.Science China. Life sciences · 2024Review
- A biosynthetic network for protoberberine production inHorticulture research · 2024Article
- Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure ofInternational journal of molecular sciences · 2023Article
- Comparative genome and metabolome analyses uncover the evolution and flavonoid biosynthesis betweeniScience · 2023Article
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis has been used as a traditional medicine for more than 2000 years in China and many other Asian countries. The pharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-quality genome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50 of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of long terminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales was discovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurine synthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected in the berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highest in the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensis provides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.
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