Genome-wide characterization and analysis of rice DUF247 gene family

TL;DR

This paper identifies and analyzes 69 DUF247 genes in rice, revealing their roles in development and stress response.

Contribution

The study provides the first comprehensive characterization of the DUF247 gene family in rice, including their phylogeny and stress-related expression.

Findings

Sixty-nine OsDUF247 genes were identified and grouped into four phylogenetic clusters.

Seven OsDUF247 genes showed stress-induced expression in rice panicles.

DUF247 proteins contain transmembrane domains, suggesting roles in rice development and environmental adaptation.

Abstract

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.

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.

These findings lay the foundation for functional characterizations of DUF247 genes to unravel their exact role in rice cultivars.

The online version contains supplementary material available at 10.1186/s12864-024-10515-8.

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