The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume

Abstract

Plant with naturally twisted branches is referred to as a tortuous-branch plant, which have extremely high ornamental value due to their zigzag shape and the natural twisting of their branches. Prunus mume is an important woody ornamental plant. However, the molecular mechanism underlying this unique trait in Prunus genus is unknown. Here, we present a chromosome-level genome assembly of the cultivated P. mume var. tortuosa created using Oxford Nanopore combined with Hi-C scaffolding, which resulted in a 237.8 Mb genome assembly being anchored onto eight pseudochromosomes. Molecular dating indicated that P. mume is the most recently differentiated species in Prunus. Genes associated with cell division, development and plant hormones play essential roles in the formation of tortuous branch trait. A putative regulatory pathway for the tortuous branch trait was constructed based on gene expression levels. Furthermore, after transferring candidate PmCYCD genes into Arabidopsis thaliana, we found that seedlings overexpressing these genes exhibited curled rosette leaves. Our results provide insights into the evolutionary history of recently differentiated species in Prunus genus, the molecular basis of stem morphology, and the molecular mechanism underlying the tortuous branch trait and highlight the utility of multi-omics in deciphering the properties of P. mume plant architecture.

Keywords: Prunus mume; genome assembly; molecular mechanism; plant architecture; tortuous branch.

Fig. 1

Synteny and distribution of genomic and epigenomic features of the Prunus mume var. tortuosa genome. (a) Flowers of P. mume var. tortuosa used in this study. (b) Tortuous branches (left) and straight branches (right) of P. mume var. tortuosa. (c) Genomic and epigenomic features of P. mume var. tortuosa. The intermediate circles from the outer circle to the inner circle (A–E) represent chromosomes, gene densities, long terminal repeats (LTRs), DNA repeats and methylation densities. The coloured lines in the centre of the circle represent synteny relationships among gene blocks.

Fig. 2

Evolution of the genome and gene families. (a) Phylogenetic tree with single‐copy orthologues from 14 species for determining divergence times. The expansion or contraction of gene families is shown via pie charts. (b) Ks distribution for orthologues between Prunus mume var. tortuosa and seven species (Fragaria vesca, Malus domestica, Rosa chinensis, P. persica, P. yedoensis, P. armeniaca and P. mume). (c) The shared and unique gene families were compared among seven closely related Rosaceae species (M. domestica, R. chinensis, P. persica, P. yedoensis, P. armeniaca, P. mume and P. mume var. tortuosa). Each number represents the number of gene families. (d) Chromosome‐level collinearity patterns between P. mume var. tortuosa and P. mume. Syntenic P. mume chromosomal regions are overlaid on the P. mume var. tortuosa chromosomes.

Fig. 3

Anatomical characteristics and transcriptomes of straight and tortuous branches of Prunus mume var. tortuosa. (a) Paraffin sections and saffron‐solid green tissue staining were used to observe cross‐sections of straight and tortuous branches. (b) Thickness of phloem and xylem in straight and tortuous stems. (c) Thickness of straight and tortuous branches along the long axis and short axis. S, straight stem; T, tortuous stem; T1, tortuous stem on the bending side; T2, tortuous stem on the opposite side. The error bars represent ± SD. (d) Venn diagram showing the shared and unique genes among the differentially expressed genes (DEGs), including those in leaf bud and stem tip samples. (e) Heatmap of the log₁₀(fold change) of all the DEGs. The rows and columns represent the genes and samples, respectively, clustered by similarity within the gene expression profile. (f) Heatmaps of −log₁₀ enrichment P‐values for the 10 most‐enriched KEGG pathways among the DEGs. LB represents the KEGG enrichment results of DEGs between the leaf buds of straight and tortuous branches. ST represents the KEGG enrichment results of DEGs between the stem tips of straight and tortuous branches.

Fig. 4

Establishment of a coexpression network. (a) Gene dendrogram and corresponding module colours. The clustering was based on the expression levels of 17 756 genes. (b) Relationships between the brown modules and expression of corresponding eigengenes across samples in the brown modules. (c) Network component analysis of proteins associated with cell division, development and plant hormones within the brown modules.

Fig. 5

Functional verification of key genes that regulate stem development. (a) Reported pathways and genes that might be involved in the regulation of stem morphology. The red‐labelled gene had collinear support and was retained in Prunus mume var. tortuosa. (b) Phylogenetic tree of CYCD genes in seven subfamilies in P. mume var. tortuosa and Arabidopsis thaliana. (c) Interaction networks of PmCYCDs and PmCDKs based on the sequences of A. thaliana orthologues in the STRING database. The red, grey, and blue colours represent upregulated, nonexpressed, and downregulated genes, respectively, in the leaf buds and stem tip samples of tortuous branches compared with straight branches. The green colour represents upregulated genes in the leaf buds and downregulated genes in the stem tips. The yellow colour represents downregulated genes in the leaf buds but upregulated genes in the stem tips. (d) Phenotype of PmCYCD1;2 OE plants compared with wild‐type (WT) plants.