| Name | Description |
|---|---|
Cnidium monnieri, a medicinal herb of the Cnidium genus and the Apiaceae family, is among the most important traditional Chinese medicines and is widely distributed in China. However, to date, no C. monnieri-related genomic information has been described. In this study, we assembled the C. monnieri genome of approximately 1210.23 Mb with a contig N50 of 83.14 Mb. Using PacBio HiFi and Hi-C sequencing data, we successfully anchored 93.86% of the assembled sequences to 10 pseudochromosomes (2n = 20). We predicted a total of 37,460 protein-coding genes, with 97.02% of them being functionally annotated in Non-Redundant, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and other databases. In addition, we identified 2,778 tRNAs, 4,180 rRNAs, 258 miRNAs, and 1,700 snRNAs in the genome. This is the first reported C. monnieri genome. Hopefully, the availability of this chromosome-level reference genome provides a significant basis for upcoming natural product-related biosynthetic pathway assessment in C. monnieri. | |
We inferred gene functions based on the best match of the alignments to the National Center for Biotechnology Information (NCBI) Non-Redundant, TrEMBL, InterPro, and Swiss-Prot protein databases using BLASTP (NCBI BLAST v2.11.0+) and the Kyoto Encyclopedia of Genes and Genomes database with an E-value threshold of 1E-5. We annotated the protein domains using PfamScan (pfamscan_version) and InterProScan (v5.50–84.0) based on the InterPro protein databases. We identified the motifs and domains within the gene models using PFAM databases. We obtained Gene Ontology IDs for each gene using Blast2GO. We functionally annotated approximately 97.02% of the predicted C. monnieri protein-coding genes with known genes, conserved domains, and Gene Ontology terms. Genome annotation has not yet been released publicly. | |
Assembly deposited as NCBI GenBank accession MT561041 View this assembly in JBrowse by visiting this page | |
Assembly deposited as NCBI GenBank accession OL839918 View this assembly in JBrowse by visiting this page |
| Name | Tissue | Treatment | Description |
|---|---|---|---|
| SAMN11356991 | leaf | Not set | |
| SAMN12280616 | Leaf | Not set | |
| SAMN12280617 | Root | Not set | |
| SAMN12280618 | Stem | Not set | |
| SAMN12280619 | Flower | Not set | |
| SAMN39465579 | aerial part | Not set |
| Accession | Accession Type |
|---|---|
| S1979_ZJ0676:EU236164 | Germplasm Accession |