Pan-Genome-Wide Characterization of the CHX Gene Family Reveals Evolutionary Dynamics and Salt-Responsive Mechanisms in Camellia

Salt stress restricts tea production by causing Na+ accumulation in leaves, disrupting K+ homeostasis, and elevating ROS levels. In Camellia, the CHX genes that may counteract these effects remain poorly defined. Using a 14-genome panel, we identified 436 CHX genes and grouped them into 26 orthologous gene groups (OGGs), including 18 core, 2 soft-core, and 6 shell. A tea-only reference captured only part of this structure; three OGGs present in 7-12 genomes were absent from tea. At the family level, dispersed and tandem duplications were the most frequent duplication classes, whereas soft-core and shell genes showed distinct duplication profiles. Among 377 high-confidence gene pairs, 98.4% had Ka/Ks values below 1, indicating that purifying selection predominates across the family. Unexpectedly, core pairs had higher Ka/Ks values than dispensable pairs. Expression analysis showed that most CHX genes were expressed at low levels across tissues. Salt treatment induced six low-abundance genes, and qRT-PCR highlighted CsCHX.CR008, CsCHX.CR012, CsCHX.SH006, and CsCHX.CR017 as priority candidates for salt-tolerance studies. Collectively, this pan-genome-scale study establishes an evolutionary framework for the CHX family in the genus Camellia, showing that duplication, presence–absence variation, copy-number variation, and conservation class are associated with distinct salt-responsive expression patterns. These findings provide genomic resources and valuable insights for dissecting CHX function and supporting future breeding efforts toward improved salt tolerance in Camellia.