# Nature Plants — Cover Letter

**Subject:** Submission of Manuscript: "ABC1K7: A 350-Myr chloroplast rheostat fine-tuned during coconut domestication"

Dear Editor,

Please find enclosed our manuscript entitled "ABC1K7: A 350-Myr chloroplast rheostat fine-tuned during coconut domestication" for consideration as an Article in Nature Plants.

Annual crop domestication is well-characterized by large-effect mutations in structural genes, but the molecular basis of perennial domestication—hypothesized to act via subtle tuning of conserved regulatory hubs ("slow variables")—has lacked direct empirical evidence. We bridge this gap by integrating 350-million-year evolutionary reconstruction with 17 years of coconut breeding panel data, identifying ABC1K7 as a deeply conserved chloroplast kinase whose single-residue substitution (Y→F) drives perennial domestication. By triangulating structural data from coconut (F652), oil palm (Y652), and date palm (Y652), we demonstrate that domestication induces a specific 5.20 Å conformational shift—exceeding the 3.07 Å baseline of natural variation between the two wild-type orthologs—thereby providing unprecedented mechanistic insight into the \"slow-variable\" theory of perennial domestication.

A single Y→F substitution in a predicted intrinsically disordered region—positioned >30 Å from the catalytic core—exhibits perfect co-segregation with dwarf stature, elevated sugar content, and thin-shell phenotypes across 327 accessions. Triangulation of PAML codon models, IQ-TREE robust phylogenetics, and protein-level inference confirms that ABC1K7 has been under extreme purifying selection (ω = 0.073–0.104) since the origin of seed plants, supporting a "canalized tinkering" model of perennial improvement. The gymnosperm outgroup *Ginkgo biloba* independently bears leucine at this position—also removing the polar hydroxyl—providing evidence of convergent regulatory attenuation across seed plant lineages.

This work provides the first molecular characterization of a slow-variable domestication target at deep evolutionary timescale, establishes a multi-model framework for studying conserved regulatory hubs, and identifies ABC1K orthologs as targets for breeding long-lived crops. We believe these findings align with Nature Plants' scope and will interest researchers across plant evolution, domestication, and sustainable agriculture.

The manuscript is original, unpublished, and not under consideration elsewhere. All authors approve its submission. Data availability complies with Springer Nature policies.

Sincerely,
Chengxu Sun, Ph.D.
Corresponding Author
Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)