Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

多倍体化是物种形成的主要驱动力，其对植物进化的重要性已得到广泛认可。竹子包括一个二倍体草本植物和三个多倍体木本植物谱系，并且是森林中多样化的草中唯一的主要亚科的成员，木本植物具有树状的木质茎秆。在这项研究中，我们生成了具有三个不同倍性水平（二倍体，四倍体和六倍体）的主要竹谱系的四个基因组草图草案。我们还构建了六倍体竹种的高密度遗传连锁图谱，并使用基于连锁图谱的策略进行基因组装配和多倍体亚基因组的鉴定。使用基于倍性水平的预期拷贝的大型同系基因数据集进行的进一步的系统生物学分析表明，木质竹子起源于草本竹谱系的发散，并通过涉及四个已灭绝的二倍体祖先的三个独立的异源多倍体事件经历了复杂的网状进化。在所有多倍体形式中鉴定出一个共享但独特的亚基因组，并且该亚基因组的祖先可能对古代多倍体化和木竹的起源至关重要。还发现了重要的遗传线索，表明竹子具有独特的开花行为和木质性状。两者合计，我们的研究为在没有现存供体物种的情况下在亚基因组水平上古代网状进化提供了重要的见识，