Fragaria vesca ‘Hawaii 4’ NAU Whole Genome v1.0 Assembly & Annotation

Analysis NameFragaria vesca ‘Hawaii 4’ NAU Whole Genome v1.0 Assembly & Annotation
MethodHifiasm (0.16.1)
SourceHiFi reads
Date performed2023-06-30


Zhou, Y., Xiong, J., Shu, Z., Dong, C., Gu, T., Sun, P., He, S., Jiang, M., Xia, Z., Xue, J., & [and other authors]. (2023). The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry. Horticulture Research, 10(4), uhad027.


Fragaria vesca, commonly known as wild or woodland strawberry, is the most widely distributed diploid Fragaria species and is native to Europe and Asia. Because of its small plant size, low heterozygosity, and relative ease of genetic transformation, F. vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011. However, its genomic contribution to octoploid cultivated strawberry remains a long-standing question. Here, we de novo assembled and annotated a telomere-to-telomere, gap-free genome of F. vesca ‘Hawaii 4’, with all seven chromosomes assembled into single contigs, providing the highest completeness and assembly quality to date. The gap-free genome is 220 785 082 bp in length and encodes 36 173 protein-coding gene models, including 1153 newly annotated genes. All 14 telomeres and seven centromeres were annotated within the seven chromosomes. Among the three previously recognized wild diploid strawberry ancestors, F. vesca, F. iinumae, and F. viridis, phylogenomic analysis showed that F. vesca and F. viridis are the ancestors of the cultivated octoploid strawberry F. × ananassa, and F. vesca is its closest relative. Three subgenomes of F. × ananassa belong to the F. vesca group, and one is sister to F. viridis. We anticipate that this high-quality, telomere-to-telomere, gap-free F. vesca genome, combined with our phylogenomic inference of the origin of cultivated strawberry, will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.


Table 2 Characteristics of the current genome assembly and previous assemblies

Genomic feature v6.0
This study
Edger et al., 2018 [11]
Tennessen et al., 2014 [15]
Shulaev et al., 2010 [10]
Genome size (Mb) 220.8 220.5 211.7 207.9
Contig N50 (Mb) 34.34 7.9   1.3 (scaffold N50)
Number of contigs 7 61 287 3200 scaffolds
Gaps 0 130 16 081 15 192
Number of telomeres 14 9 0 0
Number of centromeres 7 7 0 0
GC content (%) 38.5 38.35 35.69 34.5
Number of gene models 36 173 34 007 (v4.0.a2) 33 538 (v2.0.a2) 33 507 (v1.0 a2)
BUSCOs (%) 98.8 98.1 (v4.0.a2) 95.7 (v2.0.a2) 91.1 (v1.0 a2)



Homology of the Fragaria vesca Hawaii 4 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), 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

Fragaria vesca v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Fvesca_Hawaii4_NAU_v1.0_vs_arabidopsis.xlsx.gz
Fragaria vesca v1.0 proteins with arabidopsis (Araport11) (FASTA file) Fvesca_Hawaii4_NAU_v1.0_vs_arabidopsis_hit.fasta.gz
Fragaria vesca v1.0 proteins without arabidopsis (Araport11) (FASTA file) Fvesca_Hawaii4_NAU_v1.0_vs_arabidopsis_noHit.fasta.gz
Fragaria vesca v1.0 proteins with SwissProt homologs (EXCEL file) Fvesca_Hawaii4_NAU_v1.0_vs_swissprot.xlsx.gz
Fragaria vesca v1.0 proteins with SwissProt (FASTA file) Fvesca_Hawaii4_NAU_v1.0_vs_swissprot_hit.fasta.gz
Fragaria vesca v1.0 proteins without SwissProt (FASTA file) Fvesca_Hawaii4_NAU_v1.0_vs_swissprot_noHit.fasta.gz
Fragaria vesca v1.0 proteins with TrEMBL homologs (EXCEL file) Fvesca_Hawaii4_NAU_v1.0_vs_trembl.xlsx.gz
Fragaria vesca v1.0 proteins with TrEMBL (FASTA file) Fvesca_Hawaii4_NAU_v1.0_vs_trembl_hit.fasta.gz
Fragaria vesca v1.0 proteins without TrEMBL (FASTA file) Fvesca_Hawaii4_NAU_v1.0_vs_trembl_noHit.fasta.gz



The Fragaria vesca Hawaii Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Fvesca_Hawaii_V1.0.a1.fasta.gz


Gene Predictions

The Fragaria vesca Hawaii v1.0 genome gene prediction files are available in GFF3 and FASTA format.


Genes (GFF3 file) Fvesca_Hawaii_V1.0.a1.genes.gff3.gz
Protein sequences (FASTA file) Fvesca_Hawaii_V1.0.a1.pep.fasta.gz
CDS sequences (FASTA file) Fvesca_Hawaii_V1.0.a1.cds.fasta.gz


Functional Analysis

Functional annotation for the Fragaria vesca Hawaii 4 Genome v1.0 are available for download below. The Fragaria vesca Yanli 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 Fvesca_Hawaii4_NAU_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Fvesca_Hawaii4_NAU_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Fvesca_Hawaii4_NAU_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Fvesca_Hawaii4_NAU_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 Fragaria vesca Hawaii 4 NAU 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 Fvesca_Hawaii4_NAU_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 Fvesca_Hawaii4_NAU_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Fvesca_Hawaii4_NAU_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Fvesca_Hawaii4_NAU_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Fvesca_Hawaii4_NAU_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Fvesca_Hawaii4_NAU_v1.0_m.x.domestica_GDR_reftransV1