Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana

• Published in: BMC plant biology Vol. 23; no. 1; p. 640
• Main Authors: Akram, Jannat, Siddique, Riffat, Shafiq, Muhammad, Tabassum, Bushra, Manzoor, Muhammad Tariq, Javed, Muhammad Arshad, Anwar, Samia, Nisa, Bader Un, Saleem, Muhammad Hamzah, Javed, Bilal, Malik, Tabarak, Mustafa, Abd El-Zaher M. A., Ali, Baber
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11.12.2023; BioMed Central; BMC
• Subjects: Abscisic acid; Amino acids; Annotations; Arabidopsis thaliana; Aromatic compounds; Bioinformatics; C. sativus; Carotenoids; CCO gene family; Chitosan; Chitosan oligosaccharides; Chloroplasts; Cloning; cold stress; Comparative analysis; Cucumbers; Cucumis sativus; Cytoplasm; Enzymes; Evaluation; family; Flowers & plants; Fruits; Gene expression; gene ontology; Genes; Genetic aspects; Genome-wide association studies; genome-wide association study; Genomes; Genomics; growth and development; Hormones; Localization; Metabolism; MicroRNA; miRNA; nucleotide sequences; Oligosaccharides; Ontology; Phloem; Phloem content; Phylogenetics; Phylogeny; Physiological aspects; Phytohormones; Plant genetics; Plant growth; Plant hormones; Proteins; Regulatory sequences; RNA sequencing; strigolactones; subfamily; Synteny; transportation; Vegetables; Pakistan; CCO gene family; Chitosan oligosaccharides; Phloem content; C. sativus
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-023-04647-4

Carotenoid cleavage oxygenase (CCO) is an enzyme capable of converting carotenoids into volatile, aromatic compounds and it plays an important role in the production of two significant plant hormones, i.e., abscisic acid (ABA) and strigolactone (SL). The cucumber plant genome has not been mined for genomewide identification of the CCO gene family. In the present study, we conducted a comprehensive genome-wide analysis to identify and thoroughly examine the CCO gene family within the genomic sequence of Cucumis sativus L. A Total of 10 CCO genes were identified and mostly localized in the cytoplasm and chloroplast. The CCO gene is divided into seven subfamilies i.e. 3 NCED, 3 CCD, and 1 CCD-like (CCDL) subfamily according to phylogenetic analysis. Cis-regulatory elements (CREs) analysis revealed the elements associated with growth and development as well as reactions to phytohormonal, biotic, and abiotic stress conditions. CCOs were involved in a variety of physiological and metabolic processes, according to Gene Ontology annotation. Additionally, 10 CCO genes were regulated by 84 miRNA. The CsCCO genes had substantial purifying selection acting upon them, according to the synteny block. In addition, RNAseq analysis indicated that CsCCO genes were expressed in response to phloem transportation and treatment of chitosan oligosaccharides. CsCCD7 and CsNCED2 showed the highest gene expression in response to the exogenous application of chitosan oligosaccharides to improve cold stress in cucumbers. We also found that these genes CsCCD4a and CsCCDL-a showed the highest expression in different plant organs with respect to phloem content. The cucumber CCO gene family was the subject of the first genome-wide report in this study, which may help us better understand cucumber CCO proteins and lay the groundwork for the gene family's future cloning and functional investigations.