Prunus mume Tortuosa Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus mume Tortuosa Genome v1.0 Assembly & Annotation
Method Juicer and 3D-DNA
SourceIllumina reads
Date performed2022-03-23

Publication

Zheng T, Li P, Zhuo X, Liu W, Qiu L, Li L, Yuan C, Sun L, Zhang Z, Wang J, Cheng T, Zhang Q. The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. The New phytologist. 2021 Dec 03. doi: 10.1111/nph.17894.

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 8 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.

Assembly

The Prunus mume Tortuosa Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Pmume_Tortuosa_v1.0.fasta.gz
Repeats (GFF3 file) Pmume_Tortuosa_v1.0.repeats.gff3.gz

 

Gene Predictions

The Prunus mume Tortuosa Genome v1.0 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Pmume_Tortuosa_v1.0.proteins.fasta.gz
CDS  (FASTA file) Pmume_Tortuosa_v1.0.cds.fasta.gz
Genes (GFF3 file) Pmume_Tortuosa_v1.0.genes.gff3.gz