Supporting data for "A phased, chromosome-scale genome of ‘Honeycrisp’ apple (<i>Malus domestica</i>) "

Honeycrisp is one of the most valuable apple cultivars grown in the United States and a popular breeding parent due to its superior fruit quality traits, high levels of cold hardiness, and disease resistance. However, it suffers from a number of physiological disorders and is susceptible to production and postharvest issues. Although several apple genomes have been sequenced in the last decade, there is still a substantial knowledge gap in understanding the genetic mechanisms underlying cultivar-specific traits. Here we present a fully phased, chromosome-level genome of Honeycrisp apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms. Our genome assembly is by far the most contiguous among all the apple genomes. The sizes of the two assembled haplomes are 674 Mb and 660 Mb, with contig N50s of 32.8 Mb and 31.6 Mb, respectively. In total, 47,563 and 48,655 protein coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database, the most complete among all <i>Malus</i> annotations. A gene family analysis using seven <i>Malus</i> genomes shows that a vast majority of Honeycrisp genes are assigned into orthogroups shared with other genomes, but it also reveals 121 Honeycrisp-specific orthogroups. We provide a valuable resource for understanding the genetic basis of horticulturally important traits in apples and other related tree fruit species, including at-harvest and postharvest fruit quality, abiotic stress tolerance, and disease resistance, all of which can enhance breeding efforts in Rosaceae.

蜜脆（Honeycrisp）是美国种植的最具经济价值的苹果栽培品种之一，凭借优异的果实品质性状、极强的抗寒性与抗病性，成为广受欢迎的育种亲本。然而，该品种存在多种生理失调问题，且易受生产及采后问题困扰。尽管过去十年间已有多个苹果基因组完成测序，但针对品种特异性状的遗传机制解析仍存在显著的知识缺口。本研究基于PacBio HiFi、Omni-C及Illumina测序平台，构建了蜜脆苹果的全相型染色体级基因组。该基因组组装是目前所有苹果基因组中连续性最优的：两个组装完成的单倍型基因组大小分别为674 Mb与660 Mb，重叠群N50值分别达32.8 Mb与31.6 Mb。分别在两个单倍型基因组中注释得到47563个与48655个蛋白质编码基因，在真双子叶植物数据库中覆盖了96.8%~97.4%的完整BUSCO（Benchmarking Universal Single-Copy Orthologs），是目前苹果属（Malus）基因组注释中完整性最佳的。基于7个苹果属基因组的基因家族分析显示，绝大多数蜜脆基因可归入与其他基因组共享的正交群，但同时也鉴定出121个蜜脆特异性正交群。本研究为解析苹果及其他相关木本果树的园艺重要性状（包括采收期及采后果实品质、非生物胁迫耐受性及抗病性）的遗传基础提供了宝贵资源，这些性状可助力蔷薇科（Rosaceae）作物的育种工作。