Phased 'Golden Delicious' Apple Genome Reveals Haplotype-Specific Allelic Expression
This study presents a new haplotype-resolved, phased version of the 'Golden Delicious' apple genome, with haplotypes of 647.3 Mb and 649.2 Mb. Phasing was validated using 10,321 specific SNPs, and telomere-to-telomere continuity was checked via telomeric sequence composition. Gene prediction found 45,116 genes in haplotype 1 and 45,063 in haplotype 2. A pangenome analysis with 6 haplotype-resolved genomes identified common and unique gene families. The phased genome enabled genome-wide allele-specific expression analysis; for Md-PG1, the haplotype 2 allele (GDH2-10g24673) was the dominant contributor to total expression. The assembly also revealed specific miRNA chromosomal distribution patterns and a distinct methylation profile. These resources are proposed to aid apple breeding by illuminating allelic regulation of agronomic traits.