Genome analysis of Channel millet reveals a wild dodecaploid shaped by environmental variability

Polyploidy is a major evolutionary force generating genetic novelty over macroevolutionary scales, shaping the diversification and success of flowering plants. Channel millet, a wild C4 millet, is from semi-arid and arid inland Australia. Here we show that Channel millet is a dodecaploid by generating a high-quality, de novo, haplotype-resolved genome assembly (2.66 Gb). Subgenome-specific repetitive sequences resolve the evolutionary relationships of this allopolyploid to six ancestral progenitors. The haplotypes of each subgenome show low heterozygosity yet substantial diversity exists between subgenomes, likely underpinning the species’ ecological success and vigour. This extreme polyploidy could be an adaptation to the high environmental variation. Archaeological and ethnohistoric evidence suggests that this species has a long history of use as food, which, along with the highly variable environment, may have contributed to the evolution of this unique genome structure. The genomic complexity within the Echinochloa complex provides critical insights into wild extreme polyploid evolution. Channel millet has been traditionally used as a food source used by indigenous communities in Australia and is adapted to hot, drought-prone and saline enironments. Here, the authors report its haplotype-resolved dodecaploid genome assembly and reveal the genomic complexity within the Echinochloa complex.