| Analysis Name | Prunus mume ASM2933915v1 Assembly & Annotation |
| Sequencing technology | Illumina; Oxford Nanopore |
| Assembly method | SOAPdenovo v. MAY-2010; SMARTdenovo v. DEC-2015 |
| Release Date | 2023-03-22 |
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. New Phytol. 2022 Jul;235(1):141-156. doi: 10.1111/nph.17894.
AbstractPlant 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.
Assembly statistics
| Genome size | 237.8 Mb |
| Total ungapped length | 237.7 Mb |
| Number of chromosomes | 8 |
| Number of scaffolds | 32 |
| Scaffold N50 | 29.4 Mb |
| Scaffold L50 | 4 |
| Number of contigs | 241 |
| Contig N50 | 2.7 Mb |
| Contig L50 | 25 |
| GC percent | 37.5 |
| Genome coverage | 50.0x |
| Assembly level | Chromosome |
The Prunus mume ASM2933915v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Pmume.tuosa.HiC.fasta.gz |
The Prunus mume ASM2933915v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Pmume.tortuosa.gene.gff.gz |
| CDS sequences (FASTA file) | Pmume.tortuosa.cds.fasta.gz |
| Protein sequences (FASTA file) | Pmume.tortuosa.pep.fasta.gz |
Functional annotation for the Prunus mume ASM2933915v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Prunus_mume_Tortuosa.Pfam.tsv.gz |
Prunus S genes Nucleotide
Prunus S genes Protein