Prunus mume Tortuosa Genome v1.0 Assembly & Annotation

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


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.


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.


Homology of the Prunus mume Tortuosa Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 


Protein Homologs

Prunus mume v1.0 proteins with NCBI nr homologs (EXCEL file) pmume_Tortuosa_v1.0_vs_nr.xlsx.gz
Prunus mume v1.0 proteins with NCBI nr (FASTA file) pmume_Tortuosa_v1.0_vs_nr_hit.fasta.gz
Prunus mume v1.0 proteins without NCBI nr (FASTA file) pmume_Tortuosa_v1.0_vs_nr_noHit.fasta.gz
Prunus mume v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pmume_Tortuosa_v1.0_vs_arabidopsis.xlsx.gz
Prunus mume v1.0 proteins with arabidopsis (Araport11) (FASTA file) pmume_Tortuosa_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus mume v1.0 proteins without arabidopsis (Araport11) (FASTA file) pmume_Tortuosa_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus mume v1.0 proteins with SwissProt homologs (EXCEL file) pmume_Tortuosa_v1.0_vs_swissprot.xlsx.gz
Prunus mume v1.0 proteins with SwissProt (FASTA file) pmume_Tortuosa_v1.0_vs_swissprot_hit.fasta.gz
Prunus mume v1.0 proteins without SwissProt (FASTA file) pmume_Tortuosa_v1.0_vs_swissprot_noHit.fasta.gz
Prunus mume v1.0 proteins with TrEMBL homologs (EXCEL file) pmume_Tortuosa_v1.0_vs_trembl.xlsx.gz
Prunus mume v1.0 proteins with TrEMBL (FASTA file) pmume_Tortuosa_v1.0_vs_trembl_hit.fasta.gz
Prunus mume v1.0 proteins without TrEMBL (FASTA file) pmume_Tortuosa_v1.0_vs_trembl_noHit.fasta.gz



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


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.


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


Functional Analysis

Functional annotation for the Prunus mume Tortuosa Genome v1.0 are available for download below. The Prunus mume Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).


GO assignments from InterProScan pmume_Tortuosa_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pmume_Tortuosa_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs pmume_Tortuosa_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways pmume_Tortuosa_v1.0_KEGG-pathways.xlsx.gz


Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus mume genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.


Fragaria x ananassa GDR RefTrans v1 pmume_Tortuosa_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 pmume_Tortuosa_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 pmume_Tortuosa_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 pmume_Tortuosa_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 pmume_Tortuosa_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 pmume_Tortuosa_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 pmume_Tortuosa_v1.0_pyrus_GDR_reftransV1