Comparative Pangenomics of the MATE Family Reveals Gene Content Variation and Identifies a Citrate-Transporter-Proximal Candidate Group in Vaccinium

Plant multidrug and toxic compound extrusion (MATE) transporters participate in citrate transport, aluminium detoxification, and mineral homeostasis, yet their diversity and genomic organisation in Vaccinium remain poorly understood. In this study, we compared the MATE family across 34 blueberry and cranberry genomes and examined a candidate group related to experimentally characterised citrate transporters. The high-confidence family set contained 3479 proteins, and new MATE orthogroups continued to be detected as blueberry genomes were added. Genome searches showed that incomplete or non-standard annotations explained some of the apparent absences: four of the 12 tested orthogroups changed their prevalence category after gene-model reconstruction. In contrast, the candidate group was represented by 66 genome-supported loci, with at least one detected in each crop assembly. These loci were largely dispersed, often retained a similar neighbouring-gene order, and formed eight direct collinear links across six chromosome-scale Vaccinium genomes. A codon model estimated a global dN/dS of 0.876, which did not differ significantly from one. Comparisons of 2 kb upstream regions revealed sequence differences among the assemblies, while two public root transcriptomes showed increased expression assigned to CUFF.34706 at pH 6.5 in ‘Emerald’ and ‘Reka’. Interaction tests did not establish genotype-specific pH responses. Together, these results distinguish variable MATE gene content from a consistently detected candidate group and identify sequences for further studies of transport and regulation.