A Phased, Chromosome-scale Genome forMalus domestica ‘WA 38’

Abstract

AbstractGenome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation gives breeders, researchers, and growers information about cultivar specific traits such as fruit quality, disease resistance, and informs strategies to enhance postharvest storage. Here we present a haplotype-phased, chromosomal level, genome ofMalus domestica, ‘WA 38’, a new cultivar of apple released to market in 2017 as Cosmic Crisp ®. Using both short and long read sequencing our fully phased genome of ‘WA 38’ is about 650 Megabases, with a BUSCO score of 98.7% complete. The genome contains two haplomes (HapA and HapB) which are composed of 17 chromosomes each. A total of 48,227 and 54,479 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to ‘Gala’, ‘Honeycrisp’, and other relevant cultivars highlighting major structural and quality differences. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that included ‘WA 38’ (WSU) and the ‘d’Anjou’ pear (Auburn University). To ensure transparency, reproducibility, and applicability for any genome project, our genome assembly and annotation workflow is recorded in detail and shared under a public GitHub repository. All software is containerized, offering a simple implementation of the workflow.