Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel’s genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.

完整、准确的参考基因组和注释为功能基因组学和作物育种提供了基础资源。在这里，我们报告了豌豆品种 ZW6 的从头组装和注释，其重叠群 N50 为 8.98 Mb，与现有序列相比，其重叠群长度增加了 243 倍，复杂重复区域的序列连续性和质量明显提高。 118 种栽培豌豆和野生豌豆的基因组多样性表明， Pisum abyssinicum是不同于豌豆中的P. fulvum和P. sativum的独立物种。数量性状基因座分析发现了两个已知的与茎长度（ Le/le ）和种子形状（ R/r ）相关的孟德尔基因，以及孟德尔研究的一些与豆荚形状相关的候选基因。构建了116个豌豆材料的泛基因组，深海豌豆和黄豌豆的泛基因组表现出明显的功能富集，表明它们作为未来豌豆育种资源的潜在价值。