Improved genome assembly of double haploid Prunus persica siblings ‘Lovell 2D’ and ‘Lovell 5D’

Authors: Gottschalk, Christopher; BROCK, JORDAN - Washington University; MANSFIELD, BEN - Washington University; MAIN, DORRIE - Washington State University; JUNG, SOOK - Washington State University; ZHENG, PING - Washington State University; WHITT, LAUREN - Former ARS Employee; Vann, Cheryl; Demuth, Mark; Bennett Jr, Dennis; LIU, ZONGRANG - Retired ARS Employee; Dardick, Christopher

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2026
Publication Date: 4/21/2026
Citation: Gottschalk, C.C., Brock, J., Mansfield, B., Main, D., Jung, S., Zheng, P., Whitt, L., Vann, C.D., Demuth, M.A., Bennett Jr, D.R., Liu, Z., Dardick, C.D. 2026. Improved genome assembly of double haploid Prunus persica siblings ‘Lovell 2D’ and ‘Lovell 5D’. Scientific Reports. https://doi.org/10.1038/s41598-026-46952-6.
DOI: https://doi.org/10.1038/s41598-026-46952-6

Interpretive Summary: Peach is a high-value fruit crop grown across the US and is a critical component of human nutrition and healthy diets. Developing new peach varieties through breeding is a challenging process that requires combining numerous important tree traits such as tree size and shape, flowering time, disease and stress tolerance, as well as consumer traits including fruit size, shape, color, flavor, flesh texture, fuzziness, shelf-life and other aspects associated with eating experience. Breeders increasing rely on genetic information to help inform their efforts. The availability of the first complete DNA sequence for peach generated in 2013 has served as a tremendous tool for modern breeding for over a decade. Here we report updated peach DNA sequences generated using the latest technologies. These new versions have more complete chromosomes and provide additional critical genetic information. These updated sequences will provide the breeding and research communities with improved tools for generating new superior peach varieties to ensure the future availability of fresh, high quality fruit for US consumers.

Technical Abstract: Prunus persica (peach) has long served as a model fruit tree for studying phenological events. It has a relatively small genome and tremendous plasticity in climate tolerances due to the high variation of chill requirements, bloom times, and fruit ripening times. Peach var ‘Lovell 2D’ was among the first high-quality genomes generated for a tree species and was assembled using Sanger sequencing of genetic-map ordered BAC clones. A key to the high quality of this early version was the use of a doubled haploid variety to eliminate assembly challenges posed by sequence derived from mixed haplotypes. Here, we re-sequenced and assembled the ‘Lovell 2D’ genome along with a doubled haploid sibling ‘Lovell 5D’ using 3rd generation technologies. The resulting genomes were significantly more contiguous than the current ‘Lovell 2D’ reference genome (ver2.0 updated in 2017) and are closer to the estimated total genome size for peach (265Mb). In addition, new gene, transposable element (TE), and Nucleotide-binding domain and Leucine-rich repeat receptor (NRL) annotations were performed to enhance genome utility. These updated peach doubled-haploid reference assemblies will provide the research community with an improved reference genome for genomics-guided studies and breeding efforts.