Chromosome-scale genome assembly provides insights into speciation of allotetraploid and massive biomass accumulation of elephant grass (Pennisetum purpureum Schum.).

Elephant grass (Pennisetum purpureum Schum) is an important forage, biofuels and industrial plant widely distributed in tropical and subtropical areas globally. It is characterized with robust growth and high biomass. We sequenced its allopolyploid genome and assembled 2.07 Gb into A' and B subgenomes of 14 chromosomes with scaffold N50 of 8.47 Mb, yielding a total of 77,139 genes. The allotetraploid speciation occurred approximately 15 Ma after the divergence between Setaria italica and Pennisetum glaucum, according to a phylogenetic analysis of Pennisetum species. Double whole-genome duplication (WGD) and polyploidization events resulted in large-scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional divergence between subgenomes A' and B. A' subgenome mainly contributed to plant growth, development and photosynthesis, whereas the B subgenome was primarily responsible for effective transportation and resistance to stimulation. Some key gene families related to cellulose biosynthesis were expanded and highly expressed in stems, which could explain the high cellulose content in elephant grass. Our findings provide deep insights into genetic evolution of elephant grass and will aid future biological research and breeding, even for other grasses in the family Poaceae.