Comparative in silico analysis reveals divergent genomic features of Xa27 and Xa23 loci in indica and japonica subspecies

Rice bacterial blight resistance executor R genes, Xa27 and Xa23 , are known for conferring wide-ranging resistance to diverse Xanthomonas oryzae pv. oryzae ( Xoo ) races. Through bioinformatics approaches, we conducted an in-depth structural analysis to characterize these genes. To investigate their genomic organization, a 100 Kb gene locus flanking region was isolated. In this region, we identified and predicted a total of 13 indica -specific and 17 japonica -specific functional genes associated with Xa27 , while Xa23 exhibited 19 indica -specific and 16 japonica -specific genes. We calculated the average GC content of functional genes. For Xa27 , the average GC content was 58.01% ( indica ) and 57.06% ( japonica ), whereas Xa23 displayed 56.75% ( indica ) and 56.35% ( japonica ). Our analysis identified SSR motifs, with monomers being prevalent in both genes and cultivars. Notably, Xa23 showed a higher average percentage of SSR repeats than Xa27 . Microsynteny analysis, subcellular localization, and domain/motif identification were performed for indica and japonica cultivars of both genes. Moreover, we identified pathogen-responsive cis-acting regulatory elements (WRE3, WUN-motif, W-box) and other defense-related cis-regulatory elements in the 100 Kb flanking region of both genes. ABRE cis-acting regulatory elements were most abundant in Xa27 ( indica ) with 49 instances. Similarly, Xa23 ( indica ) exhibited the highest number of ABRE, totaling 63 occurrences. This study identified several rice genes involved in cuticular wax biosynthesis ( Os27in01, Os27in03, Os27jp01 ) and biotic/abiotic stress resistance. Genes like Os27in02, Os27jp02, Os27jp03, Os23in03 , and Os23jp02 encode serine/threonine receptor kinases critical for defense. Resistance genes Xa46 ( Os23in03, Os23jp02 ) and Xa10 ( Os23jp05 ) were found near the Xa23 locus. Strigolactone biosynthesis genes ( Os23jp13, Os23jp14 ) were also identified. Several genes bind key pathogen-responsive motifs (WRE3, WUN, W-box) and ABRE elements important for stress responses. In summary, our bioinformatics study offers comprehensive insights into the structural attributes of Xa27 and Xa23 R genes in rice. This includes gene composition, genomic characteristics, regulatory elements, and potential defense-associated mechanisms.