Objective This study focuses on the disease resistance genes of 28 vegetable crops, aiming to systematically analyze their evolutionary dynamics and expansion mechanisms, providing theoretical basis and data resources for molecular breeding of resistant vegetables.

Method Genome data for 28 vegetable crops were collected from the Published Plant Genomes website and related literature. After data verification and standardization, disease resistance genes were identified and classified using the DRAGO3 tool; phylogenetic analysis, species divergence time estimation, and gene family expansion/contraction analysis were conducted using OrthoFinder, RAxML, PAML and CAFÉ software; DIAMOND program and MCScanX software were used to identify types of disease resistance gene duplication, and SSR molecular markers were developed using MISA program and Primer3 software.

Result A total of 46 259 disease resistance genes were identified from 28 vegetable crops, with Brassica napus and Brassica oleracea ranking at the top. The family distribution is highly uneven (KIN accounts for 48.64%). Family expansion analysis shows that Brassica oleracea has expanded the most, and although Brassica napus has contracted 570 families, it achieves the highest absolute number by selectively eliminating redundant subfamilies and concentrating on expanding core families (KIN, RLK, TNL). Divergence time analysis indicates that this difference originates from genome remodeling during the divergence of the two species around 3.38 million years ago, suggesting they adopted different expansion patterns. WGD/segmental duplication is the dominant mechanism in Brassica oleracea (81.65%) and Brassica napus (76.20%), Ipomoea batatas and Solanum tuberosum exhibit a multi-mechanism collaborative pattern of tandem duplication, dispersed duplication, and WGD. SSR analysis shows the highest abundance in Ipomoea batatas, Solanum tuberosum, and Brassica rapa, with a significant proportion of the p3 type trinucleotide repeat motif. Tandem repeats may enhance SSR abundance by increasing coding region repeat sequences.

Conclusion This study constructed a standardized comparative genomics dataset for vegetable crops, clarified the evolutionary mechanisms of disease resistance gene family expansion, and provided important candidate gene targets and molecular marker resources for genetic improvement of resistant vegetables, germplasm innovation, and studies of resistance mechanisms.