Genome-wide identification, phylogenomics, and expression analysis of benzoxazinoids gene family in rice (Oryza sativa)

Benzoxazinoids (BXs) are potent secondary metabolites that affect plants' biotic and abiotic interactions. Extensive studies on the functions of benzoxazinoids in mediating biotic and abiotic stressors have been reported in maize, wheat, and rye. However, little is known about BXs biosynthesis in rice. This study presents a genome-wide analysis of forty-three Oryzae sativa BXs genes that form diphyletic clusters in a neighbor-joining tree. The first cluster comprised genes that encode the first four steps in BXs biosynthesis (BX2–BX4), leading to the production of 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA). The second cluster mainly comprised BX6 and BX7 genes responsible for BXs glycosylation. Furthermore, BXs proteins harboring similar conserved motifs were found to group according to their phylogenetic clustering. Whereas the P450 superfamily protein is conserved in BX1-BX4 proteins, the UDP-glucosyltransferase is conserved in BX7 members. These proteins were found to be strategically localized in subcellular compartments where their catalytic activities are executed. BX1 proteins are localized in the chloroplasts, where they encode the production of indole. BX6 were identified as cytoplasmic proteins, where they are involved in the hydroxylation of DIBOA-Glycoside to 2-(2,4,7-trihydroxy-8-methoxy-1,4-benzoxazine-3-one)-β-d-glucopyranose (TRIBOA-Glycoside). Further investigation of the molecular addresses showed that BXs proteins tend to localize together on chromosomes based on their functions. Moreover, the expression profiles of these proteins vary at various developmental stages in rice tissues and organs, highlighting the potential for biotic and abiotic interactions. The prospects of BXs genes in growth induction were also investigated by analyzing their responsiveness to plant hormones and nutrient treatment. BXs gene expression is affected by exogenous treatment with auxin and gibberellin as well as nitrogen, potassium, and phosphorus contents, suggesting a possible role in growth mediation. This study lays the foundation for further studies to elucidate the functions of BX genes in rice.