Convergent genome evolution reveals shared routes to salt tolerance in flowering plants

Transitions to saline environments pose formidable challenges to plants, yet halophytism has evolved independently across many flowering plant lineages. We assembled a comparative angiosperm gene catalog of ∼10 million protein-coding genes from 232 genomes spanning 55 families, with similar representation of halophytes and salt-sensitive relatives, to identify convergent genomic signatures of halophytism. Halophytes show remarkable convergence with recurrent genomic trends in salt-response genes, including lower copy numbers, higher basal expression, more constrained expression variation, distinct evolutionary rates, and independent positive selection on select genes at the same amino acid sites across multiple halophyte lineages. Crops and their wild halophytic relatives differ in gene family evolution, particularly in stress-response pathways. These findings reveal repeatedly tested evolutionary routes to halophytism and establish a genomic foundation for translating convergent adaptations into salt-tolerant crops.