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. 2021 Jun 1;8(1):121.
doi: 10.1038/s41438-021-00559-2.

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis

Da-Xia Chen #  1   2   3 , Yuan Pan #  1   2   3 , Yu Wang #  1   2   3 , Yan-Ze Cui #  4 , Ying-Jun Zhang  4 , Rang-Yu Mo  1   2   3 , Xiao-Li Wu  1   2   3 , Jun Tan  1   2   3 , Jian Zhang  1   2   3 , Lian-An Guo  1   2   3 , Xiao Zhao  1   2   3 , Wenkai Jiang  4 , Tian-Lin Sun  4 , Xiao-Di Hu  5 , Long-Yun Li  6   7   8
Affiliations

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis

Da-Xia Chen et al. Hortic Res. .

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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Conflict of interest statement

The author declares no competing interests.

Figures

Fig. 1
Fig. 1. Genome features across 9 chromosomes.
The outermost circle (blue) represents each chromosome of the genome. The bar charts of the second to fifth circles suggest gene density, LTR density, Copia and Gypsy density, respectively. The inner circular representation shows interchromosomal synteny. All sections were drawn based on window size = 300 kb and chromosome units = 500 kb
Fig. 2
Fig. 2. Comparison of gene families.
a Venn diagrams displaying the number of gene families shared among five species. b Phylogenetic tree constructed by 817 single-copy genes. The divergence time is given in millions of years in blue. The gene families that expanded and contracted are given in green and red, respectively. c, d Percentage distribution of Ks for orthologous and paralogous gene pairs. The x-axis denotes the Ks value. The y-axis denotes the percentage of gene pairs. Rate distributions were not corrected (c); Macleaya cordata rates were corrected for Coptis chinensis (d)
Fig. 3
Fig. 3. Phylogenetic analysis of LTRs in the C. chinensis genome.
The neighbor-joining phylogenetic trees based on Ty1/copia (a) and Ty3/gypsy (b). Major lineages are named, and the proportion is indicated
Fig. 4
Fig. 4. BIA biosynthesis in C. chinensis.
a Gene expression in BIA metabolism pathways. In each heatmap, the columns from left to right represent the expression level of the roots of C. chinensis from 3 to 6 years. b The magnoflorine, jatrorrhizine, columbamine, coptisine, palmatine, and berberine contents in C. chinensis roots from 3 to 6 years based on HPLC. Values are means ± SE. Values with the same letter within each BIA type are not significantly different
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