ABC1K7: A 350-Myr chloroplast rheostat fine-tuned during coconut domestication

Perennial crops follow different domestication trajectories from annuals, yet the molecular basis of slow-variable domestication—subtle tuning of conserved regulatory hubs—remains poorly characterized. We reconstructed the evolutionary history of the chloroplast kinase ABC1K7 across 9 seed plant species spanning ∼350 Myr, employing PAML codon models, IQ-TREE robust codon models, and protein-level phylogenetic inference, with AlphaFold2 structural modeling. ABC1K7 was under extreme purifying selection (ω = 0.073–0.104) across all seed plants. In coconut, a single Y→F substitution at residue 652—located >30 Å from the catalytic core in a predicted intrinsically disordered region—represents the only non-synonymous change differentiating coconut from 7 of 8 angiosperm orthologs, and exhibits perfect co-segregation with domestication traits across a 17-year breeding panel ( n = 327). These findings provide population-level evidence consistent with the slow-variable domestication model, identifying ABC1K orthologs as targets for perennial crop improvement.