The chromosome-level genome assembly of lance asiabell (Codonopsis lanceolata), a medicinal and vegetable plant of the Campanulaceae family

Abstract

Codonopsis lanceolata (2n = 2x = 16) belongs to the Campanulaceae family and is a valuable medicinal and vegetable plant primarily found in East Asia. Several studies have demonstrated its excellent pharmacological effects, for example in bronchial treatment. However, genomic information of C. lanceolata is scarce, hindering studies on crop improvement of the species. Here, we report a high-quality chromosome-level genome assembly of C. lanceolata based on a hybrid method using Nanopore long-read, Illumina short-read, and Hi-C data. The assembled genome was completed as 1,273 Mb (84.5% of the estimated genome size), containing eight pseudo-chromosomes, ranging from 101.3 to 184.3 Mb. The genome comprised of 71.3% repeat sequences and 46,005 protein-coding genes, of which 85.7% genes were functionally annotated. Completeness of the assembled genome and genes was assessed to be 97.5% and 90.4%, respectively, by Benchmarking Universal Single-Copy Orthologs analysis. Phylogenetic and synteny analysis revealed that C. lanceolata was closely related to Platycodon grandiflorus in the Campanulaceae family. Gene family evolution revealed significant expansion of related genes involved in saponin biosynthesis in the C. lanceolata genome. This is the first reference genome reported for C. lanceolata. The genomic data produced in this study will provide essential information for further research to improve this medicinal plant and will broaden the understanding of the Campanulaceae family.

First Contiguous Genome Assembly of Japanese Lady Bell (Adenophora triphylla) and Insights into Development of Different Leaf Types

“…In the BUSCO analysis, 95.6% of genes were assembled in a complete form, while 1.0% were assembled in a fragmented form. The completeness of the genome was comparable with that of four genomes reported from C. lanceolata and P. grandifloras belonging to the Campanulaceae family (Supplementary Table S5) [8][9][10]25]. The genome was completed at 2.48 Gb, comprising 8432 contigs with an N50 value of 403.7 Kb (Table 1).…”

“…Genes 2024, 15, 58 2 of 13 The genome assemblies of two species, balloon flower (Platycodon grandiflorus) [8,9] and lance asiabell (Codonopsis lanceolate) [10], belonging to the Campanulaceae family, have been previously reported. However, the genome assembly of Japanese lady bell has not yet been reported.…”

Genome-Wide Comparative Profiles of Triterpenoid Biosynthesis Genes in Ginseng and Pseudo Ginseng Medicinal Plants

“…Nine assembled genomes (five species from Panax (i.e., Panax ginseng (PAGI0), Panax notoginseng (PANO0), Panax japonicus (PAJA0), Panax stipuleanatus (PAST0), and Panax quinquefolius (PAQU0) [14])) and Pseudo ginseng (Codonopsis lanceolata (COLA0) [23], Platycodon grandiflorus (PLGR0) [24], Gynostemma pentaphyllum (GYPE0) [25], and outlier Daucus carota (DACA0)) were selected and downloaded from the Refseq assembly database. The respective annotations were obtained from the corresponding authors via email request [14,[23][24][25].…”

“…When looking at the BUSCO completeness assessments, P. ginseng, P. japonicus, and P. quinquefolius had more duplicated core genes than the others. This is due to the ploidy nature of the genus and the assembled genomes [23,24,40,41]. This may influence the high transcript isoforms in the gene/transcript numbers in genome annotation compared to others.…”

“…This may influence the high transcript isoforms in the gene/transcript numbers in genome annotation compared to others. It is worth noting that these Pseudo ginseng plants are widely used as an alternative for ginseng due to the saponin content present in their roots, making them popular in the traditional medicinal market [23,24,40].…”