Genome-wide identification and expression profiling of the GYF gene family in Vanilla planifolia: insights into fruit development and Cymbidium mosaic virus response

Introduction Vanilla planifolia is a tropical crop producing high-value natural vanilla flavor but suffers chronic yield losses from Cymbidium mosaic virus (CymMV), a potexvirus for which resistance sources are limited and durable genetic resistance is not currently available. GYF (glycine-tyrosine-phenylalanine) domain proteins regulate mRNA surveillance, translational control, and immunity across eukaryotes. In Arabidopsis, the GYF protein EXA1 functions as a potexvirus susceptibility factor; however, no genome-wide analysis of the GYF gene family has been reported for V. planifolia . Methods We performed genome-wide identification of GYF genes in the haplotype-phased V. planifolia genome using HMM profiling, BLASTP, and domain annotation. Phylogenetic, syntenic, and promoter cis-element analyses were conducted. Transcriptome data from fruits of high- and low-vanillin accessions were analyzed. CymMV inoculation experiments were performed over nine weeks, with viral accumulation confirmed by coat-protein transcript quantification and gene expression monitored by qRT-PCR. Results We identified 11 GYF loci represented by 22 haplotype-specific allelic copies (VpGYF1–VpGYF22). Phylogenetic analysis grouped them into three clades corresponding to ATXR3/ATXR7 SET–GYF chromatin regulators (Clade I), NERD-like multi-domain proteins (Clade II), and EXA1-like translational regulators (Clade III). Ka/Ks ratios indicated purifying selection. Promoter analysis identified abundant SA-, MeJA-, and ethylene-responsive elements alongside WRKY, MYB, and MYC/bHLH sites. VpGYF expression in fruits correlated with vanillin content, with higher expression in glucovanillin-rich inner white tissue. Following CymMV inoculation, VpGYF genes showed broad transcriptional responsiveness, with the strongest induction in VpGYF4/GYF12, VpGYF19/GYF21, and VpGYF6/GYF14. Discussion These results implicate VpGYF genes in both secondary metabolism and potexvirus host interactions in vanilla. The infection-responsive loci are prioritized as candidates for functional validation and host factor–based resistance strategies.