Genome-wide identification and in silico expression analysis of CCO gene family in Citrus sinensis (orange) in response to citrus greening

<i>Citrus sinensis</i> (L.) Osbeck (sweet orange) is the most important cultivated citrus fruit in the world. However, Hanglongbing (HLB) disease, caused by <i>Candidatus Liberibactor asiaticus</i> (CLAs), poses a major threat to sweet orange production, by hindering colour, quality and export. Carotenoid cleavage oxygenases (CCOs), which include carotenoid cleavage dioxygenases (CCDs) and 9-cis-epoxycarotenoid dioxygenases (NCEDs), are essential for plant growth, development, and adaptation to phytohormonal, biotic, and abiotic stresses. This study identified 14<i>CsCCO </i>genes in <i>C. sinensis.</i> Structural and conservation studies were conducted using gene structure and conserved domain analysis. Genomic localisation, gene duplication, and similarity among these genes were also examined. Gene ontology analysis predicted that CsCCOs could be involved in the carotene catabolic process. Analysis of cis-regulatory elements revealed that most <i>CsCCO</i> genes are involved in responses to stress, light signalling, and plant growth regulation. Genes in the 9-cis-epoxycarotenoid dioxygenase (NCED) subgroup are predominantly localised in chloroplasts, whereas genes in other subgroups are primarily found in the cytoplasm. All 13 of the <i>CsCCOs</i> genes identified were regulated by 25microRNAs, indicating the crucial role of microRNAs in gene regulation in <i>Citrus sinensis</i>. The expression patterns of <i>CsCCO</i> genes in response to biotic and abiotic stress were studied. Transcriptome analysis demonstrated that <i>CsNCED3</i> and <i>CsNCED10 </i>were up-regulated in response to HLB. This provides insight into the function of <i>CCO</i> genes in <i>C. sinensis</i> and identifies potential candidate genes for combating citrus greening.