A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

Abstract

SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.

Genome of the North American wild apple speciesMalus angustifolia

“…Our approach to scaffolding was replicated from Mansfeld et al (2023). In short, the draft haplotype assemblies were scaffolded using Chromonomer (v.1.13) with linkage maps markers sourced from M. × domestica (Bianco et al, 2014;Di Pierro et al, 2016;Catchen et al, 2020).…”

“…The pairwise comparison order was determined based on the phylogenetic analyses outlined above. The comparison sequence involved the M. angustifolia haplotype 1 assembly being compared to M. fusca haplotype 1 (Mansfeld et al, 2023), followed by a comparison of M. fusca to M. sieversii haploid, then M. sieversii to M. sylvestris haploid (Sun et al, 2020), and finally M. sylvestris to the M. × domestica genome cv. 'Honeycrisp' haplotype 1 (Khan et al, 2022).…”

“…To annotate the long-terminal repeat (LTR) retrotransposon space, we employed a pan-genome approach within the EDTA software package (Ou et al, 2019). This approach was successfully used to annotate the M. fusca v1.1 genome (Mansfeld et al, 2023). We identified that each M. angustifolia haplotype assembly contained 58.6% LTRs (Table 2), roughly 4% more than the smaller genomes of its other wild relatives.…”

“…Resistance to fire blight has been observed by most of the USDA accessions (Dougherty et al, 2021;Khan & Chao, 2017;Emeriewen et al, 2014). Our recent exploration into the Pacific Crabapple, Malus fusca, genome suggests that this co-evolution in North America likely manifested as presence and absence variation of G-type receptor like genes, at a known resistance locus for fire blight, which may contribute to resistance to this disease (Mansfeld et al, 2023). Thus, the North American wild Malus relatives are poised to act as a crucial and valuable trove of genetics to improve apple resistance to biotic and resilience abiotic threats.…”

“…To address some of these challenges related to the integration of wild apple genes into apple cultivation, considerable efforts have been directed toward sequencing and assembling wild Malus genomes and developing other genomic tools that can facilitate the use of wild Malus species in cultivar enhancement (Mansfeld et al, 2023;Ruhsam et al, 2022;Li et al, 2022;Sun et al, 2020;Chen et al, 2019). As part of our effort to continue to explore and develop genomes of North American Malus species, we herein report the high-quality diploid genome assembly and annotation of M. angustifolia accession PI 613880.…”