Cross-species dissection of saline-related genes by genetically deciphering a euryhaline microalga Chlorella sp

Deciphering adaptation to habitat shifts across the salinity boundary necessitates investigation of “lost” and “acquired” saline genes. By assembling a telomere-to-telomere genome, we propose that the euryhaline Chlorophyta Chlorella sp. MEM25 represents an early-diverging saltwater species that has evolved numerous genes essential for saltwater-freshwater transitions. By comparison with Viridiplantae genomes, we identify ancestral genes and lineage-specific genes related to salinity adaptation. Loss-of-function mutants of the proposed salt-sensitive genes in algae and plants exhibit increased salt resistance, highlighting the potential of the MEM25 genome as a breeding resource. Notably, the gene RMI1 plays an important role in salinity tolerance across species, from microalgae to higher plants.