The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth.

Elephant grass (2n = 4x = 28; Cenchrus purpureus Schumach.), also known as Napier grass, is an important forage grass and potential energy crop in tropical and subtropical regions of Asia, Africa and America. However, no study has yet reported a genome assembly for elephant grass at the chromosome scale. Here, we report a high-quality chromosome-scale genome of elephant grass with a total size of 1.97 Gb and a 1.5% heterozygosity rate, obtained using short-read sequencing, single-molecule long-read sequencing and Hi-C chromosome conformation capture. Evolutionary analysis showed that subgenome A' of elephant grass and pearl millet may have originated from a common ancestor more than 3.22 million years ago (MYA). Further, allotetraploid formation occurred at approximately 6.61 MYA. Syntenic analyses within elephant grass and with other grass species indicated that elephant grass has experienced chromosomal rearrangements. We found that some key enzyme-encoding gene families related to the biosynthesis of anthocyanidins and flavonoids were expanded and highly expressed in leaves, which probably drives the production of these major anthocyanidin compounds and explains why this elephant grass cultivar has a high anthocyanidin content. In addition, we found a high copy number and transcript levels of genes involved in C photosynthesis and hormone signal transduction pathways that may contribute to the fast growth of elephant grass. The availability of elephant grass genome data advances our knowledge of the genetic evolution of elephant grass and will contribute to further biological research and breeding as well as for other polyploid plants in the genus Cenchrus.