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

Abstract

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. 104,957 and 102,356 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 medium‐density genotyping platform for cultivated strawberry using DArTag technology

“…The recent availability of high‐quality reference genomes and sequence datasets for strawberry has provided essential resources for trait mapping, functional genomics, and genetic marker development in this allo‐octoploid hybrid species (Bassil et al., 2015; Edger et al., 2019; Hardigan et al., 2020, 2021; Lee et al., 2021; Hardigan et al., 2021; Mao et al., 2023; Shirasawa et al., 2021). The growing molecular breeding toolbox for strawberry has nevertheless needed cost‐effective high‐throughput marker genotyping solutions to enable genomic selection and routine forensic identification of individuals and parents on a large scale (Gezan et al., 2017; Jiménez et al., 2023; Osorio et al., 2021; Pincot et al., 2020, 2021; Whitaker et al., 2020).…”

“…The publication of multiple single nucleotide polymorphism (SNP) arrays for strawberry from 2015 to 2020 enabled genetic and physical mapping of new loci controlling traits related to disease resistance and fruit quality (Bassil et al., 2015; Barbey et al., 2021; Castillejo et al., 2020; Jiménez et al., 2023; Noh et al., 2018; Nelson et al., 2021; Nellist et al., 2019; Oh et al., 2019; Osorio et al., 2021; Oh et al., 2021; Pincot et al., 2018, 2020, 2021, 2022; Pillet et al., 2017; Petrasch et al., 2022; Salinas et al., 2019). Progress in this area has only increased following the publication of multiple high‐quality, chromosome‐scale assemblies of octoploid Fragaria genomes in the last 5 years (Edger et al., 2019; Hardigan et al., 2021; Lee et al., 2021; Mao et al., 2023; Shirasawa et al., 2021). These genome assemblies, in combination with resequencing, genomic variant calling, and linkage mapping have demonstrated that strawberry contains mainly diploid‐behaving subgenomes with sufficient sequence divergence, in many cases, to allow targeting of specific homeologous sites for marker genotyping and, potentially, future CRISPR editing (Hardigan et al., 2020, 2021; Ledda et al., 2019).…”

Transcriptome analysis of fruit development and identification of key transcription factors related to anthocyanin pathway in cultivated octoploid strawberry

“…Total RNA was extracted from different-stage fruits using the CTAB method (Lei et al 2020). The library for RNA sequencing was constructed as described by Mao et al 2023. The RNA-seq data were uploaded to NCBI and the accession number is PRJNA975298.…”

“…In addition, Lin et al (2021) also found some key regulators with anthocyanin synthesis in strawberries through transcriptome sequencing without the reference genome. Recently, our team assembled a haplotype-resolved genome of cultivated octoploid strawberries (Mao et al 2023). This study identi ed crucial genes involved in anthocyanin synthesis in cultivated strawberries based on the transcriptome data and the haplotyperesolved genome of cultivated octoploid strawberries.…”

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

“…Genome sequence further enabled the design of a single nucleotide polymorphism (SNP) 50K array with selected chromosome-specific SNPs 21 allowing the high-resolution mapping of QTLs. A recent breakthrough has been the completion of haplotype-resolved genomes for five genotypes of F. × ananassa 9,22,23,24,25 . These developments make it possible to exploit strawberry diversity through genome wide association studies (GWAS), which scans the genome for significant associations between genetic markers and the trait studied 2 .…”