Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.

Background: Nudix hydrolases (NHs), characterized by the conserved Nudix motif (GX₅EX₇REUXEEXGU), hydrolyze nucleoside diphosphate derivatives and play vital roles in plant stress responses and cellular homeostasis. However, the NH gene family has not been systematically characterized in maize (Zea mays L.). Methods: We performed a genome-wide analysis of ZmNH (Nudix hydrolase) genes using a maize pan-genome encompassing 26 high-quality genomes. Results: A total of 73 ZmNH members were identified, comprising 22 core genes (present in all 26 lines), 28 dispensable genes (present in 2–25 lines), and 23 private genes (present in only one line). Phylogenetic analysis clustered them into three subgroups (Type-I, -II, and -III), with Type-III being the largest (28 members). Gene structure and motif analyses revealed conserved exon–intron architectures and 10 conserved motifs. Nonsynonymous/synonymous substitution ratio (Ka/Ks) calculations across the 26 inbred lines indicated that most ZmNH genes were under purifying selection (Ka/Ks < 1), whereas ZmNH2 and ZmNH12 showed evidence of positive selection in some lines. Expression profiling under four stress conditions—Fusarium graminearum, Cercospora zeina, Exserohilum turcicum, and Ostrinia furnacalis—identified 20 differentially expressed ZmNH genes. Notably, ZmNH9 was consistently responsive across multiple pathogen treatments, suggesting a potential role in broad-spectrum disease resistance. Conclusions: These findings provide a foundation for future functional studies of the maize NH gene family.