Prunus campanulata Genome v1.0 Assembly & Annotation

Analysis NamePrunus campanulata Genome v1.0 Assembly & Annotation
MethodHifiasm (v0.8)
SourcePacBio HiFi reads for Pcampanulata
Date performed2023-10-18


Hu, Y., Feng, C., Wu, B., & Kang, M. (2023). A chromosome-scale assembly of the early-flowering Prunus campanulata and comparative genomics of cherries. Scientific Data, 10, 920.


Prunus campanulata is an important flowering cherry germplasm of high ornamental value. Given its early-flowering phenotypes, P. campanulata could be used for molecular breeding of ornamental species and fruit crops belonging to the subgenus Cerasus. Here, we report a chromosome-scale assembly of P. campanulata with a genome size of 282.6 Mb and a contig N50 length of 12.04 Mb. The genome contained 24,861 protein-coding genes, of which 24,749 genes (99.5%) were functionally annotated, and 148.20 Mb (52.4%) of the assembled sequences are repetitive sequences. A combination of genomic and population genomic analyses revealed a number of genes under positive selection or accelerated molecular evolution in P. campanulata. Our study provides a reliable genome resource, and lays a solid foundation for genetic improvement of flowering cherry germplasm.


Genome assembly

For PacBio SMRT sequencing, the PacBio Sequel II platform was first used to generate sub-reads, and the sub-reads were then filtered by the ccs software using the parameter “min-passes=3, min-rq=0.99” to obtain 27.50 Gb of Hifi reads. The PacBio HiFi reads were assembled into the initial set of contigs using hifiasm v0.816 with default parameters. The contig assembly had a total size of ~282.6 Mb, with a contig N50 value of 12.04 Mb. To achieve chromosome-level assembly, the ALLHiC algorithm was used to group, adjust the order and orientation of contigs and anchor the assembled contigs into eight pseudomolecules based on Hi-C data. After ALLHiC scaffolding, Hi-C interaction heat map was constructed using HiC-Pro v3.1.0 and visualized using HiCPlotter.

Genome annotations

For repeat sequence annotation, we used a combined strategy of homology-based search and de novo prediction. The homology-based search was based on the Repbase database using RepeatMasker ( and RepeatProteinMask ( to search for interspersed repeat elements. The de novo prediction was based on a species-specific repeat database generated by LTR_FINDER, Piler , RepeatScout and RepeatModeler. Using this library, we identified de novo involved repeats with RepeatMasker and predicted tandem repeats with TRF. In addition, we used RepeatMasker to mask the repetitive sequences as input for gene structure prediction.

For protein-coding gene structure prediction, we used a comprehensive approach that integrates homology-based prediction, de novo prediction, and RNA-Seq-based prediction. For homology-based prediction, Blast and Genewise were used to align the amino acid sequences from the Malus domestica, P. serrulata, Vitis vinifera, A. thaliana, and P. salicina genomes to the assembled P. campanulata sequences. Augustus, GlimmerHMM, SNAP, GeneID, and GenScan were used to predict de novo gene models. Cufflinks and PASA were applied to predict the gene models in the RNA-Seq-based prediction study. The results of the above three approaches were further integrated to generate a final non-redundant gene model set using EVidenceModeler and modified using PASA.


Homology of the Prunus campanulata 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-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

Prunus campanulata v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pcampanulata_v1.0_vs_arabidopsis.xlsx.gz
Prunus campanulata v1.0 proteins with arabidopsis (Araport11) (FASTA file) Pcampanulata_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus campanulata v1.0 proteins without arabidopsis (Araport11) (FASTA file) Pcampanulata_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus campanulata v1.0 proteins with SwissProt homologs (EXCEL file) Pcampanulata_v1.0_vs_swissprot.xlsx.gz
Prunus campanulata v1.0 proteins with SwissProt (FASTA file) Pcampanulata_v1.0_vs_swissprot_hit.fasta.gz
Prunus campanulata v1.0 proteins without SwissProt (FASTA file) Pcampanulata_v1.0_vs_swissprot_noHit.fasta.gz
Prunus campanulata v1.0 proteins with TrEMBL homologs (EXCEL file) Pcampanulata_v1.0_vs_trembl.xlsx.gz
Prunus campanulata v1.0 proteins with TrEMBL (FASTA file) Pcampanulata_v1.0_vs_trembl_hit.fasta.gz
Prunus campanulata v1.0 proteins without TrEMBL (FASTA file) Pcampanulata_v1.0_vs_trembl_noHit.fasta.gz

The Prunus campanulata genome v1.0 assembly files are available in GFF3 and FASTA format.


Chromosomes (FASTA file) Pcampanulata_V1.fasta.gz
Repeats (GFF3 file) Pcampanulata_V1.repeats.gff.gz
Gene Predictions

The Prunus campanulata genome v1.0 gene prediction files are available in GFF3 and FASTA format.


Genes (GFF3 file) Pcampanulata_V1.genes.gff3.gz
Protein sequences (FASTA file) Pcampanulata_V1.pep.fasta.gz
CDS sequences (FASTA file) Pcampanulata_V1.cds.fasta.gz
Functional Analysis

Functional annotation for the Prunus campanulata Genome v1.0 are available for download below. The Prunus campanulata 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 Pcampanulata_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Pcampanulata_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Pcampanulata_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Pcampanulata_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 campanulata 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 Pcampanulata_v1.0_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pcampanulata_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pcampanulata_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pcampanulata_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pcampanulata_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Pcampanulata_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Pcampanulata_v1.0_pyrus_GDR_reftransV1