Malus x domestica Antonovka 172670-B Whole Genome v1.0 Assembly & Annotation

Publication

Švara, A., Sun, H., Fei, Z., & Khan, A. (2023). Chromosome-level phased genome assembly of 'Antonovka' identified candidate apple scab resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1. G3 Genes|Genomes|Genetics, https://doi.org/10.1093/g3journal/jkad253

Abstract

Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6 scab resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab resistance loci Vhc1 in ‘Honeycrisp’ and Rvi17 in ‘Antonovka’, were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in ‘Honeycrisp’ and ‘Antonovka’. Previously published chromosome-scale phased assembly of ‘Honeycrisp’ and a newly assembled phased genome of ‘Antonovka’ 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with eight available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87-95% and 81-95%, respectively. Among these homologs, two candidate genes in ‘Antonovka’ and ‘Honeycrisp’ haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1, and identifies candidate genes for further resistance characterization.

Table 1. Summary statistics for phased chromosome-level genome assembly of ‘Antonovka’ apples. BUSCO: Benchmarking Universal 20 Single-Copy Orthologs; bp: base pairs; QV: Quality value.