Genomes of Meniocus linifolius and Tetracme quadricornis unveil the ancestral karyotype and genomic features of core Brassicaceae

Brassicaceae represents an important family at both scientific and economic levels. However, genomic features coupled to the early diversification of this family have not been fully characterized especially upon the uplift of the Tibetan Plateau followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, via analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E) together with genomes representing all major Brassicaceae clades and the basal Aethionemeae, we identified the genomic architecture accompanying early Brassicaceae diversification. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing nine pseudochromosomes with 65 conserved syntenic genomic blocks (GBs) and identified 9,702 conserved genes for Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well to the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes that play essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified and followed by divergent expression. Our results provide fresh insights into historical genomic features coupled to Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under ever-changing environment.