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

Abstract 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.