Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata)

Abstract

Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.

Fig. 1

Morphological characters (a) and the landscape of genome assembly and annotation of M. paniculata (b). The tracks from outside to inside are: pseudo-chromosomes, density of class I TEs, density of class II TEs, density of protein-coding genes, proportion of tandem repeats, GC content and collinear blocks.

Fig. 2

Venn diagram showing the unique and shared functionally annotated protein-coding genes in M. paniculata using the three strategies.

Fig. 3

Telomere distribution (a) and comparation of genome structure between haplotype A and haplotype B (b).

Fig. 4

Copy number spectra plots for genome (a), haplotype A (b) and haplotype B (c) using KAT (K-mer Analysis Toolkit). The k-mers from HiFi reads display two dominant heterozygous (multiplicity = 18) and homozygous (multiplicity = 34) peaks, and those from assemblies have 0–6×+ copy numbers.

Fig. 5

Hi-C interaction heatmap of haplotype A and haplotype B with reads mapping quality ≥0 (including duplicated reads) (a) and mapping quality ≥1 (excluding duplicated reads) (b). The colour bar indicates the strength of the interaction, with yellow representing low and red representing high.