1 College of Bioscience and Resources Environment,Beijing University of Agriculture, Beijing 102206, China; 2 Institute of Biotechnology/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; 3 School of Life Sciences, Hebei University, Baoding 071002, China
Abstract：Peach (Prunus persica) is a model species for genetic and genomic research within the Rosaceae family. China is the geographical origin of peach, and maintains the richest diversity of peach germplasm worldwide. Founder parents play a critical role in breeding programs, and their genome sequences offer basis insights into the genetic mechanisms underlying key horticultural traits. To investigate the basic genomicinformation of peach founder parents, over 1 000 pedigree records were analyzed, and the Japanese cultivar 'Okubo' and the American cultivar 'Legrand' were identified as key founder parents, with their generational relationships within breeding pedigree clarified. Combining assembly of sequenced reads from third-generation sequencing technology Oxford Nanopore Technologies (ONT) with the second-generation sequencing technology Illumina, high-quality, chromosome-scale genome assemblies for 'Okubo' (Okubo v1.0; 238.19 Mb) and 'Legrand' (Legrand v1.0; 238.57 Mb) were generated by combining assembly of sequenced reads from third-generation sequencing technology Oxford Nanopore Technologies (ONT) with second-generation sequencing technology Illumina, with Contig N50 lengths of 9.95 and 14.97 Mb, with mapping back rates of 99.71% and 99.32%, and GC contents of 37.55% and 37.57%, respectively. The genome assembly quality assessment benchmarking universal single-copy orthologs (BUSCO) value was of 98.8%, the long-terminal-repeat assembly index (LAI) value was of 29.13 and 27.46, and the second-generation short read alignment rates was of 99.30% and 99.85% for 'Okubo' and 'Legrand', respectively. Through genomic repeat element annotation, 47.01% and 52.15% repetitive sequences were identified in Okubo v1.0 and Legrand v1.0, respectively, included retroelements (20.20% and 18.95%) and DNA transposons (11.73% and 11.75%). A total of 23 503 ('Okubo') and 22 062 ('Legrand') protein-coding genes were annotated based on integrated genomic annotation strategy of de novo prediction, homology-based methods, and transcriptome data evidence, among which 81.04% and 81.03% of genes were assigned by functional annotation. Comparative genomic analysis revealed 91.83% for 'Okubo' and 89.36% for 'Legrand' of collinearity between the reference Lovell v2.0 genome, and identified 20.71 and 16.36 Mb of divergent regions in 'Okubo' and 'Legrand', respectively, encompassing 2 319 and 1 493 genes enriched in functions related to binding, catalytic activity, and metabolic processe. This study identified peach founder parents through pedigree analysis, with 2 cultivars subjected to in-depth genome sequencing, high-quality genome assembly, gene annotation, and comparative genomic analysis against reference genomes. These efforts provide backbone genomes for peach pan-genomics research, facilitating genetic dissection and improvement of important agronomic traits while advancing comparative genomics within the Rosaceae family.
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