A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa

Abstract

Chaenomeles speciosa (2n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.

Figure 1

Genome survey and assembly of Chaenomeles speciosa. (A) Greenish fruits, (B) collinearity of the two sets of C. speciosa haploid chromosomes. The collinearity is based on telomere, repeat sequence distribution, and gene density between the two sets of chromosomes. (C) High-quality genome assembly of C. speciosa. The genome diagram features five circles. The outmost greenish circle comprises 17 chromosomes. The remaining circles represent distributions of genes, transposons, telomere repeats, and GC content along with the chromosomes. The center represents the synteny blocks among the chromosomes. (D) Plot showing heterozygosity resulting from k-mer analysis. (E) Plot showing the similarity of syntenies between the genomes of apple and C. speciosa.

Figure 2

Orthologous clustering and phylogenetic analysis of the Chaenomeles speciosa genome. (A) The flower-shaped diagram shows the core orthogroup (in the center) shared by C. speciosa and 10 other plant species and 11 petal parts formed by 11 species-specific orthogroups. (B) Enrichment analysis via KEGG characterizes that expanded gene families in the C. speciosa genome are associated with 17 different functions. (C) A phylogenetic tree developed from 11 genomes shows the lines of evolutionary descent relationship among C. speciosa and 10 other species. The numbers at branch nodes indicate the divergence time. The pie charts inserted in each branch show the relative genome size expansion (the right-side color block) and contraction (the left-side color block). The numbers of gene family expanded (+) and contracted (−) in each plant species were placed on the right.

Figure 3

Features of whole genome duplication (WGD), synteny, and chromosome evolution of Chaenomeles speciosa. (A) The contents of repetitive sequences were compared in the genomes of Vitis vinifera, Rosa chinensis, Prunus armeniaca, Prunus persica, Pyrus communis, C. speciosa, and Malus domestica. (B) The LTR insertion times were compared in V. vinifera, R. chinensis, P. armeniaca, P. persica, P. communis, C. speciosa, and M. domestica. (C) A plot shows features resulted from self-collinearity analysis of C. speciosa. (D) A phylogenetic tree was developed with six species in Rosaceae. (E) A diagram was created from the intergenomic co-linearity analysis of R. chinensis, P. armeniaca, P. persica, P. communis, C. speciosa, M. domestica. (F) Plots show the synonymous substitutions per synonymous site (Ks) distributions of R. chinensis, P. armeniaca, P. persica, P. communis, C. speciosa, and M. domestica.

Figure 4

Proposed biosynthetic pathways of oleanolic acid and ursolic acid and beta-amyrin synthase gene clusters in Chaenomeles speciosa. (A) Numbers of genes encoding enzymes of the biosynthetic pathway of oleanolic acid and ursolic acid in eight plants. Those Arabic numerals included in each box above each arrow are member numbers in each gene family encoding the enzyme in Malus domestica, Prunus armeniaca, Prunus persica, Prunus yedoensis, Pyrus betulifolia, Pyrus communis, Rosa chinensis, and C. speciosa. (B) and (C) Distribution of two beta-amyrin synthase gene clusters on C. speciosa chromosome 9.