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

Authors

You, N., Chen, Y., John, M., Zhou, N., Li, W., Cao, H., Sun, C.

Abstract

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 (omega = 0.073-0.104) across all seed plants. In coconut, a single Y to F substitution at residue 652 - located >30 A 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.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 10 Aug 2026.

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