背景回顾：Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. 

提出问题：Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts.

主要研究：To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. 

结果1-基因渐滲：Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. 

结果2-病虫害抗性：Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. 

结论：Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

基于基因组的生物技术使得加速长寿的多年生作物育种成为可能。尽管分子工具在山核桃和其他异交树种中具有改造潜力，但高度杂合的基因组、显著的存在-缺失基因含量变异和种间杂交的历史限制了这些树种的育种工作。为了克服这些障碍，作者在本文中对四个远缘杂交山核桃基因型进行了全基因组测序、组装和注释，并且对栽培种“Pawnee”的两套单倍型进行了基于PacBio HiFi的染色体级别组装。比较分析和泛基因组揭示了大量可能的适应性种间基因组滲入，包括一个从苦味胡桃中渗入山核桃育种谱系的，被过多保留下来的单倍型。此外，通过利用不同基因组之间和“Lakota”基因组的两套单倍型之间的存在-缺失和功能注释数据库，作者鉴定了山核桃中作用于病虫害抗性的候选基因。综上，本文的研究在高度多态性和远缘杂交作物的功能和数量基因组学方面取得了重大进展。