High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry

Cultivated strawberry(Fragaria×ananassa),a perennial herb belonging to the family Rosaceae,is a complex octoploid with high heterozygosity at most loci.However,there is no research on the haplotype of the octoploid strawberry genome.Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar,“Yanli”,using single molecule real-time sequencing and high-throughput chromosome conformation capture technology.The“Yanli”genome was 823 Mb in size,with a long terminal repeat assembly index of 14.99.The genome was phased into two haplotypes,Hap1(825 Mb with contig N50 of 26.70 Mb)and Hap2(808 Mb with contig N50 of 27.51 Mb).Using the combination of Hap1 and Hap2,we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry.We identified a∼10 Mb inversion and translocation on chromosome 2-1.104957 and 102356 protein-coding genes were annotated in Hap1 and Hap2,respectively.Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F.×ananassa genome.In summary,we obtained a high-quality haplotype-resolved genome assembly of F.×ananassa,which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.

A splice site mutation in the FvePHP gene is associated with leaf development and f lowering time in woodland strawberry

Leaves and f lowers are crucial for the growth and development of higher plants.In this study we identified a mutant with narrow leaf lets and early f lowering(nlef)in an ethyl methanesulfonate-mutagenized population of woodland strawberry(Fragaria vesca)and aimed to identify the candidate gene.Genetic analysis revealed that a single recessive gene,nlef,controlled the mutant phenotype.We found that FvH4_1g25470,which encodes a putative DNA polymeraseαwith a polymerase and histidinol phosphatase domain(PHP),might be the candidate gene,using bulked segregant analysis with whole-genome sequencing,molecular markers,and cloning analyses.A splice donor site mutation(C to T)at the 5-end of the second intron led to an erroneous splice event that reduced the expression level of the full-length transcript of FvePHP in mutant plants.FvePHP was localized in the nucleus and was highly expressed in leaves.Silencing of FvePHP using the virus-induced gene silencing method resulted in partial developmental defects in strawberry leaves.Overexpression of the FvePHP gene can largely restore the mutant phenotype.The expression levels of FveSEP1,FveSEP3,FveAP1,FveFUL,and FveFT were higher in the mutants than those in‘Yellow Wonder’plants,probably contributing to the early f lowering phenotype in mutant plants.Our results indicate that mutation in FvePHP is associated with multiple developmental pathways.These results aid in understanding the role of DNA polymerase in strawberry development.