A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. ‘ WA 38’
A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. ‘ WA 38’
Abstract Genome 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 of Malus domestica, ‘WA 38’, a new apple cultivar released to market in 2017 as Cosmic Crisp ?. Using both short and long read sequencing data with a k-mer based approach, chromosomes originating from each parent were assembled and segregated. This is the first pome fruit genome fully phased into parental haplotypes in which chromosomes from each parent are identified and separated into their unique, respective haplomes. The two haplome assemblies, ‘Honeycrisp’ originated HapA and ‘Enterprise’ originated HapB, are about 650 Megabases each, and both have a BUSCO score of 98.7% complete. A total of 53,028 and 54,235 genes were annotated from HapA and HapB, respectively. Additionally, we provide genome-scale comparisons to ‘Gala’, ‘Honeycrisp’, and other relevant cultivars highlighting major differences in genome structure and gene family circumscription. This assembly and annotation was done in collaboration with the American Campus Tree Genomes project that includes ‘WA 38’ (Washington State University), ‘d’Anjou’ pear (Auburn University), and many more. 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 GitLab repository. All software is containerized, offering a simple implementation of the workflow.
Ko Itsuhiro、Eaker Abigail、Haney Sabrina、Ryan Kara、Appleby Aaron B.、Hoffmann Brendan、Landis Henry、Yocca Alan、Pierro Kenneth、Willsea Noah、Honaas Loren、Harkess Alex、Khuu Ninh、Hargarten Heidi、Zhang Huiting、Ficklin Stephen
Department of Plant Pathology, Washington State University. Pullman||Program of Molecular Plant Sciences, Washington State UniversityDepartment of Plant Pathology, Washington State University. Pullman||Program of Molecular Plant Sciences, Washington State UniversityDepartment of Animal Science, Washington State UniversityDepartment of Crop and Soil Science, Washington State UniversityIntegrated Plant Sciences Program, Washington State UniversityUSDA Agricultural Research Service||HudsonAlpha Institute for BiotechnologyIntegrated Plant Sciences Program, Washington State UniversityDepartment of Horticulture, WSU Tree Fruit Research and Extension CenterUSDA Agricultural Research ServiceHudsonAlpha Institute for BiotechnologyDepartment of Plant Pathology, Washington State University. PullmanUSDA Agricultural Research ServiceDepartment of Horticulture, Washington State University||USDA Agricultural Research ServiceDepartment of Horticulture, Washington State University
农业科学技术发展植物学生物科学研究方法、生物科学研究技术
Apple genomicsMalus domestica ‘WA 38’genome sequencecomparative genomicsplant genomicshaplotype-resolved assemblygenome annotation
Ko Itsuhiro,Eaker Abigail,Haney Sabrina,Ryan Kara,Appleby Aaron B.,Hoffmann Brendan,Landis Henry,Yocca Alan,Pierro Kenneth,Willsea Noah,Honaas Loren,Harkess Alex,Khuu Ninh,Hargarten Heidi,Zhang Huiting,Ficklin Stephen.A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. ‘ WA 38’[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2024.01.10.574953.点此复制
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