Chromosome-level Streptochaeta genome elucidates the ancestral karyotype and allopolyploid origin of grasses.

Grasses (Poaceae) are the most economically important group of plants. Reconstructing the ancestral grass genome and studying the evolutionary factors shaping major grass lineages are crucial for understanding the evolution of cereals, including rice, wheat and maize. Here, we report a chromosome-level genome assembly of Streptochaeta spicata, which represents the lineage without typical spikelets and the sister to the rest of Poaceae, and perform comparative genomic analyses across major grass lineages. We confirm the occurrence of the ρ-whole-genome duplication (ρ-WGD) in Streptochaeta, suggesting a shared allotetraploidization event for all extant grasses. Reconstruction of the ancestral grass karyotype (AGK) reveals a chromosome number of ante-ρ (x = 8) and post-ρ (x = 12), followed by chromosome number reduction by fusion events accompanying the diversification within major subfamilies. Biased subgenome fractionation and dominance are observed and inherited across Streptochaeta and major grass lineages. Comparative expression analyses of key floral genes in S. spicata indicate that the spikelet equivalent of this early-diverging lineage might represent a modified ancestral state of grass spikelet. Given its critical phylogenetic position, the Streptochaeta genome sheds light on the early karyotypic evolution of grasses, and the origin and key morphological innovation with respect to WGDs.