A curated genome-wide catalog of U-box/PUB genes in Astragalus membranaceus var. mongholicus reveals evolutionary diversification and root salt-stress-associated candidates

Abstract Background Plant U-box proteins (PUBs) are E3 ubiquitin ligases that participate in protein turnover, development, hormone signaling, immunity, and stress responses. Astragalus membranaceus var. mongholicus is an important medicinal legume whose root is the principal medicinal organ, but its PUB gene family has not been systematically characterized in a curated gene-level framework. Results Integrated U-box domain detection, homology searches, conserved-domain validation, and gene-level curation identified 64 non-redundant AmPUB genes. Phylogenetic, motif, gene-structure, and domain-architecture analyses revealed structural and evolutionary diversification of the AmPUB family. MCScanX identified 18 segmental/WGD-associated duplicated pairs, three tandem duplicated pairs, and 341 cross-species syntenic pairs across six reference species. Database-derived root transcript abundance profiles based on transcripts per million (TPM) values informed candidate selection. qRT-PCR profiling of selected candidates under salt treatment provided exploratory transcriptional evidence for subsequent functional investigation. Conclusions This study provides a curated AmPUB catalog, evolutionary context, and a refined candidate-prioritization framework for U-box/PUB genes associated with root salt-stress responses in A. membranaceus var. mongholicus . The results provide a reproducible resource for future functional studies of PUB E3 ubiquitin ligases in this medicinal legume.