Czech J. Genet. Plant Breed., 2025, 61(3):113-127 | DOI: 10.17221/11/2025-CJGPB

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

Sadaf Sarwar¹, Muhammad Shafiq¹, Layba Tasawar¹, Iram Gull², Jannat Akram³, Maha Al-Roshdi⁴, Gabrijel Ondrasek⁵, Muhammad Shafiq Shahid ORCID...^6*

¹ Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan

² School of Biochemistry & Biotechnology University of the Punjab, Lahore, Pakistan

³ Department of Plant Breeding and Genetics, University of the Punjab, Lahore, Pakistan

⁴ Department of Biological Sciences and Chemistry, College of Arts and Sciences, Nizwa University, Nizwa, Oman

⁵ Faculty of Agriculture, University of Zagreb, Zagreb, Croatia

⁶ Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman

Citrus sinensis (L.) Osbeck (sweet orange) is the most important cultivated citrus fruit in the world. However, Hanglongbing (HLB) disease, caused by Candidatus Liberibactor asiaticus (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 CsCCO genes in C. sinensis. 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 CsCCO 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 CsCCOs genes identified were regulated by 25 microRNAs, indicating the crucial role of microRNAs in gene regulation in Citrus sinensis. The expression patterns of CsCCO genes in response to biotic and abiotic stress were studied. Transcriptome analysis demonstrated that CsNCED3 and CsNCED10 were up-regulated in response to HLB. This provides insight into the function of CCO genes in C. sinensis and identifies potential candidate genes for combating citrus greening.

Keywords: 9-cis-epoxycarotenoid cleavage dioxygenases; abscisic acid (ABA); CCDs; CCOs; carotenoid cleavage dioxygenases; carotenoid cleavage oxygenases; NCEDs

Received: February 20, 2025; Revised: April 23, 2025; Accepted: April 23, 2025; Prepublished online: May 30, 2025; Published: September 5, 2025  Show citation