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

Abstract

How do plants repeatedly evolve the ability to thrive in saline environments? We analyzed ~10 million protein-coding genes from 232 angiosperm genomes spanning 55 families to identify convergent genomic signatures of halophytism. Across lineages, halophytes exhibit recurrent patterns in salt-response genes, including reduced gene numbers, higher basal expression, and constrained expression variation. We identified distinct evolutionary rate patterns and independent positive selection at the same amino acid sites across halophytes, revealing molecular convergence. Comparisons of crops and their wild halophytic relatives uncover contrasting gene family trajectories in stress-response pathways. These findings challenge the idea that increased gene number is the predominant route to adaptation and reveal recurrent genomic strategies associated with halophytism, advancing understanding of convergent evolution and providing a foundation for developing salt-tolerant crops.