Pan-genome-wide characterization of the ascorbate peroxidase gene family reveals evolutionary dynamics and salt-responsive mechanisms in Fraxinus

Fraxinus species exhibit considerable variation in salt tolerance, with Fraxinus velutina showing exceptional adaptation to saline-alkaline environments. Ascorbate peroxidase (APX) plays a central role in reactive oxygen species scavenging under salt stress; however, a comprehensive pan-genome analysis of APX family evolution in Fraxinus has not yet been conducted. Using the pan-genome comprising 11 Fraxinus species, we identified 118–140 APX genes and clustered them into 121 orthologous gene groups (OGGs), including 67 core, 7 soft-core, 36 shell, and 11 lineage-specific/cloud OGGs, thus establishing the complete APX repertoire in Fraxinus. Phylogenetic and gene-structure analyses indicated that dispersed duplication acted as the primary driver of family expansion. Transposable element (TE) annotation showed that 97.58% of APXs contained complete TEs within ± 2 kb of their loci. Moreover, APXs with copy-number variation (CNV) carried significantly more TEs than non-CNV APXs, implicating TE activity in CNV formation. Dispensable APXs exhibited higher Ka, Ks, and Ka/Ks values than core APXs, suggesting relaxed selective pressures. Integrative transcriptome analyses demonstrated widespread APX activation under salt treatment, with different OGGs induced at distinct time points, indicating temporal functional divergence. This pan-genome-scale investigation establishes a comprehensive evolutionary framework for the APX gene family in Fraxinus. Our findings elucidate APX expansion patterns, highlight TE-associated CNV dynamics, and reveal diverse transcriptional responses to salt stress, thereby providing valuable insights and genomic resources for understanding APX-mediated salt tolerance and supporting future breeding efforts.