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.

Decoding the molecular regulation mechanism of plant architecture in woody plants

“…Therefore, decoding the complicated molecular basis underlying this phenomenon is economically valuable, scientifically interesting and also tremendously challenging (Kucukoglu et al, 2017). In this issue of New Phytologist, Zheng et al (2022; pp. 141-156) utilized a genomics approach to identify candidate genes related to the tortuous-branch phenotype in Prunus mume (Fig.…”

“…Because of their unique ornamental properties, cultivation of tortuous-branch plants has become an important direction in the process of P. mume reproduction. Zheng et al (2022) achieved de novo genome assembly of the first cultivated variety 'Yudie Longyou' using Oxford Nanopore sequencing. With high coverage of multiple types of sequencing reads, including Oxford Nanopore, BGI-seq and Hi-C data, they assembled, polished and scaffolded a high-quality haplotype-resolved genome with a size of 237.7 MB (scaffold N50: 29.4 MB), containing a total of 29 706 protein-coding genes.…”

“…tortuosa stems. Zheng et al (2022) compared the gene expression levels of leaf buds and stem tips between straight and tortuous branches using RNA-sequencing. A total of 453 and 450 differentially expressed genes (DEGs) were identified in the leaf bud (straight vs tortuous) and stem tip (straight vs tortuous) samples, respectively.…”

“…Further research found that PmCYCD plays an important role in the development of stem morphology. Zheng et al (2022) constructed four PmCYCD (PmCYCD1;1, PmCYCD1;2, PmCYCD2;1 and PmCYCD3;1) plant expression vectors and transformed them into the Arabidopsis thaliana genome. PmCYCD1;2-overexpressing seedlings showed curled rosette leaves and abnormal vascular cambium compared to the control plants.…”

“…The relatively small, diploid genome of this species, along with its unique plant architecture, make it a valuable resource for studying the evolutionary history of recently differentiated species in the genus Prunus, the molecular basis of stem morphology and decoding the molecular mechanism underlying the tortuous-branch trait. The genomic information provided by Zheng et al (2022) helps us take an important step in these directions.…”