Fragaria moupinensis haplotype Genome v1.0 Assembly & Annotation

Analysis NameFragaria moupinensis haplotype Genome v1.0 Assembly & Annotation
MethodHifiasm (v0.16.1-R375)
SourcePacbio reads
Date performed2024-01-17

Publication: Qiao, Q., Cao, Q., Zhang, R., Wu, M., Zheng, Y., Xue, L., Lei, J., Sun, H., Liston, A., & Zhang, T. (2024). Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). Plant Biotechnology Journal. Advance online publication.


The strawberry genus, Fragaria, exhibits a wide range of sexual systems and natural ploidy variation. Nearly, all polyploid strawberry species exhibit separate sexes (dioecy). Research has identified the sex-determining sequences as roughly conserved but with repeatedly changed genomic locations across octoploid strawberries. However, it remains unclear whether tetraploid wild strawberries evolved dioecy independently or shared a common origin with octoploid strawberries. In this study, we investigated the sex determinants of F. moupinensis, a dioecious plant with heterogametic females (ZW). Utilizing a combination of haplotype-resolved genome sequencing of the female F. moupinensis, k-mer-based and coverage-based genome-wide association studies (GWAS), and transcriptomic analysis, we discovered a non-recombining, approximately 33.6 kb W-specific region on chromosome 2a. Within this region, only one candidate sex-determining gene (FmoAFT) was identified. Furthermore, an extensive resequencing of the entire Fragaria genus indicated that the W-specific region displays conservative female specificity across all tetraploid species. This observation suggests that dioecy evolved independently in tetraploid and octoploid strawberries. Moreover, employing virus-induced gene silencing (VIGS), we knocked down the expression of the FmoAFT homologue transcript in cultivated strawberries, revealing its potential role in promoting female functions during early carpel development. We also applied DNA affinity purification sequencing (DAP-seq) and yeast one-hybrid assays to identify potential direct targets of FmoAFT. These insights shed new light on the genetic basis and evolutionary history of sex determination in strawberries, thereby facilitating the formulation of strategies to manipulate sex determination in breeding programs.


The Fragaria moupinensis genome v1.0 assembly files are available in GFF3 and FASTA format.


Chromosomes (FASTA file) fmoupinensis_YUN_v1.fasta.gz
Repeats (GFF3 file) fmoupinensis_YUN_v1.repeats.gff.gz
Gene Predictions

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


Genes (GFF3 file) fmoupinensis_YUN_v1.genes.gff3.gz
Protein sequences (FASTA file) fmoupinensis_YUN_v1.pep.fasta.gz
CDS sequences (FASTA file) fmoupinensis_YUN_v1.cds.fasta.gz