Genome-wide characterization and analysis of rice DUF247 gene family

Abstract

Abstract Background The domain of unknown function 247 (DUF247) proteins is involved in plant development and stress response. Rice is an important worldwide cereal crop, although an increasing number of DUF proteins have been identified, the understanding of DUF proteins is still very limited in rice. Results In this study, we identified 69 genes that encode DUF247 proteins in the rice (Oryza sativa) genome by homology searches and domain prediction. All the OsDUF247 proteins were classified into four major groups (I, II, III and IV) by phylogenetic analysis. Remarkably, OsDUF247 genes clustered on the chromosomes solely show close phylogenetic relationships, suggesting that gene duplications have driven the expansion of the DUF247 gene family in the rice genome. Tissue profile analysis showed that most DUF247 genes expressed at constitutive levels in seedlings, roots, stems, and leaves, except for seven genes (LOC_Os01g21670, LOC_Os03g19700, LOC_Os05g04060, LOC_Os08g26820, LOC_Os08g26840, LOC_Os08g26850 and LOC_Os09g13410) in panicles. These seven genes were induced by various abiotic stress, including cold, drought, heat, hormone treatment, and especially salt, as demonstrated by further experimental analysis. DUF247 proteins contain transmembrane domains located on the membrane, suggesting their significant roles in rice development and adaptation to the environment. Conclusions These findings lay the foundation for functional characterizations of DUF247 genes to unravel their exact role in rice cultivars.

Keywords

• DUF247 gene family
• Gene characterization
• Phylogenetic analysis
• Expression pattern
• Abiotic stress
• Rice