In this project, we generated draft genomes with Illumina sequencing technology from four bamboo species, Bonia amplexicaulis (Bam，hexaploid), Guadua angustifolia (Gan，tetraploid), Olyra latifolia (Ola，diploid), and Raddia guianensis (Rgu，diploid). O.latifolia and R. guianensis are herbaceous bamboos like grasses while B. amplexicaulis is paleotropical woody bamboo and G. angustifolia is neotropical woody bamboo. The assembled genome sequences are 848 Mb, 1,614 Mb, 646 Mb, and 626 Mb in length for B. amplexicaulis, G. angustifolia, O. latifolia, and R. guianensis, respectively. Genome annotations predict 47,056 protein-coding genes in B. amplexicaulis, 38,575 in G. angustifolia, 36,578 in O. latifolia, and 24,275 in R. guianensis.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise of one diploid herbaceous and three polyploid woody lineages, and are the only major subfamily in grasses which diversified in forests with tree-like lignified culm for its woody members. Here we generated four draft genomes of major bamboo lineages at three different ploidy levels (diploid, tetraploid and hexaploid). We also constructed a high-density genetic linkage map of bamboo for a hexaploid species, providing a linkage-map-based strategy for assembly and identification of subgenomes in polyploids. Further phylogenomic analyses based on a large dataset of syntenic genes with expected copies revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution by three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and its progenitor could be critical in ancient polyploidizations and origin of woody bamboos. We also found important genetic clues to the unique flowering behavior and woody trait in bamboos. 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 a broad-scale study of plant origins by allopolyploidization in angiosperms.