Chromosome-Scale Genome Assembly and Triterpenoid Saponin Biosynthesis in Korean Bellflower (Platycodon grandiflorum)

Abstract

Platycodon grandiflorum belongs to the Campanulaceae family and is an important medicinal and food plant in East Asia. However, on the whole, the genome evolution of P. grandiflorum and the molecular basis of its major biochemical pathways are poorly understood. We reported a chromosome-scale genome assembly of P. grandiflorum based on a hybrid method using Oxford Nanopore Technologies, Illumina sequences, and high-throughput chromosome conformation capture (Hi-C) analysis. The assembled genome was finalized as 574 Mb, containing 41,355 protein-coding genes, and the genome completeness was assessed as 97.6% using a Benchmarking Universal Single-Copy Orthologs analysis. The P. grandiflorum genome comprises nine pseudo-chromosomes with 56.9% repeat sequences, and the transcriptome analysis revealed an expansion of the 14 beta-amylin genes related to triterpenoid saponin biosynthesis. Our findings provide an understanding of P. grandiflorum genome evolution and enable genomic-assisted breeding for the mass production of important components such as triterpenoid saponins.

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).…”

“…A total of 70 genes were identified to be related to triterpenoid saponin biosynthesis in A. triphylla using the KEGG database (Supplementary Table S14). Triterpenoid saponins play an important role in determining the quality of medicinal plants belonging to the Campanulaceae family [39], and bASs are important oxidosqualene cyclases involved in triterpenoid saponin biosynthesis [25]. Therefore, the identified 22 bAS genes among the 70 genes involved in triterpenoid saponin synthesis provide evidence of their major contribution to triterpenoid saponin modifications in A. triphylla.…”

“…To determine the evolutionary relationship between A. triphylla and four other whole plant genomes (C. lanceolata, P. grandiflorus, Panax ginseng, and Arabidopsis thaliana) [10,25,33,34], we performed similarity-based gene clustering analysis. The genomes of A. thaliana and P. ginseng were added to investigate the evolutionary divergence of plants belonging to the Campanulaceae family (Supplementary Table S9).…”

“…In the Campanulaceae family, triterpenoid saponin pathways have been studied with diverse skeleton structures in α-amyrin, β-amyrin, dammarenediol, and lupeol metabolism [24]. In particular, β-amyrin synthase (bAS) gene families are key players in triterpenoid saponin biosynthesis [25]. However, triterpenoid saponin pathways in A. triphylla are not well characterized [26].…”

Genome-wide identification of bZIP transcription factors and their expression analysis in Platycodon grandiflorus under abiotic stress

“…Reports on bZIP genes have now been carried out in a wide variety plants, However, it is unclear whether bZIP genes are participating in the growth process of P. grandiflorus and their role in responding to abiotic stress. At present, the chromosome-scale genome of P. grandiflorus has been released ( Lee et al., 2023 ). Therefore, explore the possible role of bZIP TFs in the growth, development, and abiotic stress of P. grandiflorus on the basis of genome-wide and transcriptome data is of great significance.…”