【摘要】 桃(Prunus persica)是蔷薇科果树遗传学和基因组学研究的模式植物之一。我国是桃的原产地，拥有最为丰富的桃种质资源。骨干亲本在育种中起着重要作用，其基因组序列可为优异性状形成的遗传机制的解析奠定基础。为了解桃骨干亲本基因组基本信息，本研究对千余份桃品种资源系谱记录进行分析，明确了日本品种’Okubo’(’大久保’)与美国品种’Legrand’(’丽格兰特’)是重要的骨干亲本，展示了其品种间传代关系；通过Oxford Nanopore Technologies (ONT)三代结合Illumina二代测序技术进行测序和组装，获得’Okubo’和’Legrand’基因组Okubo v1.0和Legrand v1.0，大小分别约为238.19和238.57 Mb,Contig N50分别为9.95和14.97 Mb，染色体挂载率分别为99.71%和99.32%,GC含量分别为37.55%和37.57%；基因组质量评估值基准通用单拷贝直系同源基因(benchmarking universal single-copy orthologs, BUSCO)都为98.8%，长末端重复组装指数(long terminal repeat assembly index, LAI)值分别为29.13和27.46，二代序列比对率分别为99.30%与99.85%。通过基因组重复元件注释，Okubo v1.0和Legrand v1.0分别共鉴定出重复序列为47.01%和52.15%，其中逆转录元件分别占20.20%和18.95%,DNA转座子分别占11.73%与11.75%；采用从头预测、同源比对和转录组数据相结合的策略，分别注释出23 503和22 062个基因，其中81.04%和81.03%有功能注释。比较基因组学分析发现，Okubo v1.0和Legrand v1.0与参考基因组Lovell v2.0的共线性比例分别为91.83%和89.36%，变异区分别为20.71与16.36 Mb，分别包含2 319和1 493个基因，这些基因主要涉及结合作用、催化活性和代谢过程等方面的功能。本研究通过系谱分析鉴定了桃骨干亲本，并将其中2个重要品种进行了基因组深度测序、高质量基因组组装、基因注释和与参考基因组比较基因组学研究，为桃物种泛基因组学研究提供骨架基因组，有利于促进多种重要农艺性状遗传解析和改良及蔷薇科家族比较基因组研究。更多还原

【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 of98.8%, the long-terminal-repeat assembly index(LAI) value was of 29.13 and 27.46, and the secondgeneration 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.更多还原