Genetic Characterization of RNA Recognition Motif (RRM)-Containing Genes in Coconut Palm

RNA recognition motif (RRM)-containing proteins are important regulators involved in diverse cellular processes, including splicing, stability, transport, and translation of transcripts. However, their comprehensive characterization remains limited in perennial tropical crops like <i>Cocos nucifera</i>. In this study, we performed a genome-wide analysis of RRM genes in coconut, identifying a total of 326 <i>CnRRM</i> genes. Phylogenetic classification based on complete RRM domain sequences grouped these proteins into eleven clades (I-XI), each exhibiting distinct variations in motif length and domain architecture. Transcriptome profiling revealed diverse expression patterns across coconut tissues, ranging from constitutive to highly tissue-specific. The <i>CnHRLP1</i> gene, encoding an hnRNP-like multi-RRM protein, was selected for further functional analysis. Subcellular localization showed that the CnHRLP1 protein is predominantly nuclear, and its constitutive overexpression in <i>Arabidopsis</i> led to a severe dwarf phenotype. RNA-seq analysis demonstrated that <i>CnHRLP1</i> overexpression broadly reshaped the transcriptome. KEGG pathway enrichment highlighted a significant impact on plant hormone signaling, particularly the gibberellin (GA) pathway. <i>CnHRLP1</i> overexpression induced the coordinated downregulation of key GA biosynthetic genes (<i>KO</i>, <i>KAO1</i>/<i>2</i>, <i>GA20ox</i>, <i>GA3ox</i>) and the upregulation of GA catabolic genes (<i>GA2ox2</i>/<i>6</i>), suggesting its role in modulating GA homeostasis. In conclusion, this study provides a genomic and functional overview of the coconut RRM protein family and establishes that the hnRNP-like protein CnHRLP1 functions as a transcriptional regulator that inhibits vegetative growth, potentially through the suppression of gibberellin biosynthesis.