Compact Retention and Lineage-Specific Sequence Divergence of ALMT Genes in Acidophilic Vaccinium

This is the authors' abstract. We don't add key points for this paper.

Aluminum-activated malate transporter (ALMT) channels mediate root malate efflux, a key response for plant survival in acidic, aluminum-toxic soils. The acidophilic genus Vaccinium is horticulturally important, yet its ALMT family has remained uncharacterized. Leveraging two newly available chromosome-level genomes (Vaccinium darrowii and Vaccinium duclouxii), we present the first genus-wide characterization of this family. Across 11 angiosperms we identified 145 non-redundant ALMT loci, partitioned into six major subfamilies. MCScanX synteny revealed compact retention rather than expansion: diploid Vaccinium genomes encode only 8–10 ALMTs each, with at most one intra-species syntenic paralog pair, versus multiple whole-genome-duplication-derived pairs in apple (Malus domestica, 24 loci). Pairwise Ka/Ks was elevated within Vaccinium in three subfamilies, and codon-based PAML branch-site tests detected Bonferroni-significant positive selection on terminal Vaccinium branches in Subfamilies 5 and 4 (2ΔlnL = 40.65 and 12.95), yielding three Bayes Empirical Bayes candidate sites in Subfamily 5 (F249, E410, L411) and two in Subfamily 4 (E249, G399); Subfamily 2 was non-significant and is interpreted as relaxed constraint. All candidate residues map to C-terminal cytoplasmic regulatory regions rather than the transmembrane pore. These findings indicate that the compact Vaccinium ALMT repertoire retained its ancestral channel architecture while accumulating lineage-associated divergence in cytoplasmic regulatory regions; the identified residues are candidates for downstream functional validation rather than demonstrated drivers of acid-soil adaptation.