Fragaria x ananassa 'Florida Brilliance' Genome v1.0 Assembly & Annotation

Overview
Analysis NameFragaria x ananassa 'Florida Brilliance' Genome v1.0 Assembly & Annotation
MethodHifiasm (0.16.1)
SourceFaFB1 HiFi and Hi-C reads
Date performed2022-09-19

Publication

Han, H., Salinas, N., Barbey, C. R., Jang, Y. J., Fan, Z., Verma, S., Whitaker, V. M., & Lee, S. (2025). A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance. GigaScience. GigaScience, Volume 14, 2025, giaf005, https://doi.org/10.1093/gigascience/giaf005 

The data set is made available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.

Abstract

Background
Cultivated strawberry (Fragaria xananassa Duch.), an allo-octoploid species arising from at least 3 diploid progenitors, poses a challenge for genomic analysis due to its high levels of heterozygosity and the complex nature of its polyploid genome.

Results
This study developed the complete haplotype-phased genome sequence from a short-day strawberry, ‘Florida Brilliance’ without parental data, assembling 56 chromosomes from telomere to telomere. This assembly was achieved with high-fidelity long reads and high-throughput chromatic capture sequencing (Hi-C). The centromere core regions and 96,104 genes were annotated using long-read isoform RNA sequencing. Using the high quality of the haplotype-phased reference genome, FaFB1, we identified the causal mutation within the gene encoding Leaf Rust 10 Disease-Resistance Locus Receptor-like Protein Kinase (LRK10) that confers resistance to anthracnose fruit rot (AFR). This disease is caused by the Colletotrichum acutatum species complex and results in significant economic losses in strawberry production. Comparison of resistant and susceptible haplotype assemblies and full-length transcript data revealed a 29-bp insertion at the first exon of the susceptible allele, leading to a premature stop codon and loss of gene function. The functional role of LRK10 in resistance to AFR was validated using a simplified Agrobacterium-based transformation method for transient gene expression analysis in strawberry fruits. Transient knockdown and overexpression of LRK10 in fruit indicate a key role for LRK10 in AFR resistance in strawberry.

Conclusions
The FaFB1 assembly along with other resources will be valuable for the discovery of additional candidate genes associated with disease resistance and fruit quality, which will not only advance our understanding of genes and their functions but also facilitate advancements in genome editing in strawberry.

Table 1:   Statistics of the ‘Florida Brilliance’ genome assembly and annotation

Assembly metrics
Value
 
Haplotype-1
Haplotype-2
Final assembly
 
 
 Assembled genome size (Mb)
784.9
781.0
 Number of anchored contigs
137
86
 BUSCO (%)
99.1
99.1
  Single
2.5
2.3
  Duplicated
96.6
96.8
  Fragmented
0
0.1
  Missing
0.9
0.8
Assembly

The Fragaria x ananassa Florida Brilliance v1.0 assembly files files are available in GFF3 and FASTA formats. From each of the 28 parental pairs of octoploid strawberry chromosomes we selected the most contiguous pseudomolecule from the corresponding phase-1/phase-2 parents sets to produce an optimal haploid genome assembly labelled ‘FaFB1’.

Downloads

Chromosomes (FaFB1 non-masked)(FASTA file) FaFB1_v1.0.fasta.gz
Chromosomes (FaFB1 hard-masked)(FASTA file) FaFB1_masked_v1.0.fasta.gz
Chromosomes (FaFB1 soft-masked)(FASTA file) FaFB1_soft_masked_v1.0.fasta.gz
Chromosomes (Phase-1 non-masked)(FASTA file) Phase-1_v1.0.fasta.gz
Chromosomes (Phase-1 hard-masked)(FASTA file) Phase-1_masked_v1.0.fasta.gz
Chromosomes (Phase-1 soft-masked)(FASTA file) Phase-1_soft_masked_v1.0.fasta.gz
Chromosomes (Phase-2 non-masked)(FASTA file) Phase-2_v1.0.fasta.gz
Chromosomes (Phase-2 hard-masked)(FASTA file) Phase-2_masked_v1.0.fasta.gz
Chromosomes (Phase-2 soft-masked)(FASTA file) Phase-2_soft_masked_v1.0.fasta.gz
Gene Predictions

The Fragaria x ananassa Florida Brilliance v1.0 genome gene prediction files are available in GFF3 and FASTA formats.

Downloads

Genes (FaFB1 GFF3 file) FaFB1_v1.0.genes.gff3.gz
Gene sequences (FaFB1 FASTA file) FaFB1_v1.0.gene.fasta.gz
mRNA sequences (FaFB1 FASTA file) FaFB1_v1.0.mRNA.fasta.gz
Protein sequences (FaFB1 FASTA file) FaFB1_v1.0.protein.fasta.gz
Genes (Phase-1 GFF3 file) Phase-1_v1.0.genes.gff3.gz
Gene sequences (Phase-1 FASTA file) Phase-1_v1.0.gene.fasta.gz
mRNA sequences (Phase-1 FASTA file) Phase-1_v1.0.mRNA.fasta.gz
Protein sequences (Phase-1 FASTA file) Phase-1_v1.0.protein.fasta.gz
Genes (Phase-2 GFF3 file) Phase-2_v1.0.genes.gff3.gz
Gene sequences (Phase-2 FASTA file) Phase-2_v1.0.gene.fasta.gz
mRNA sequences (Phase-2 FASTA file) Phase-2_v1.0.mRNA.fasta.gz
Protein sequences (Phase-2 FASTA file) Phase-2_v1.0.protein.fasta.gz