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A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. 'WA 38'.

Authors :
Zhang, Huiting
Ko, Itsuhiro
Eaker, Abigail
Haney, Sabrina
Khuu, Ninh
Ryan, Kara
Appleby, Aaron B
Hoffmann, Brendan
Landis, Henry
Pierro, Kenneth A
Willsea, Noah
Hargarten, Heidi
Yocca, Alan E
Harkess, Alex
Honaas, Loren
Ficklin, Stephen
Source :
G3: Genes | Genomes | Genetics. Dec2024, Vol. 14 Issue 12, p1-17. 17p.
Publication Year :
2024

Abstract

Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation give breeders, researchers, and growers information about cultivar-specific traits such as fruit quality and disease resistance, and inform 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. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
21601836
Volume :
14
Issue :
12
Database :
Academic Search Index
Journal :
G3: Genes | Genomes | Genetics
Publication Type :
Academic Journal
Accession number :
181969539
Full Text :
https://doi.org/10.1093/g3journal/jkae222