Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana
Abstract 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 m...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-023-04647-4 |
| _version_ | 1797388404675051520 |
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| author | Jannat Akram Riffat Siddique Muhammad Shafiq Bushra Tabassum Muhammad Tariq Manzoor Muhammad Arshad Javed Samia Anwar Bader Un Nisa Muhammad Hamzah Saleem Bilal Javed Tabarak Malik Abd El-Zaher M. A. Mustafa Baber Ali |
| author_facet | Jannat Akram Riffat Siddique Muhammad Shafiq Bushra Tabassum Muhammad Tariq Manzoor Muhammad Arshad Javed Samia Anwar Bader Un Nisa Muhammad Hamzah Saleem Bilal Javed Tabarak Malik Abd El-Zaher M. A. Mustafa Baber Ali |
| author_sort | Jannat Akram |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-08T22:40:21Z |
| format | Article |
| id | doaj.art-59efd24905884ccd965730820a4d9c17 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-08T22:40:21Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-59efd24905884ccd965730820a4d9c172023-12-17T12:11:58ZengBMCBMC Plant Biology1471-22292023-12-0123111810.1186/s12870-023-04647-4Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thalianaJannat Akram0Riffat Siddique1Muhammad Shafiq2Bushra Tabassum3Muhammad Tariq Manzoor4Muhammad Arshad Javed5Samia Anwar6Bader Un Nisa7Muhammad Hamzah Saleem8Bilal Javed9Tabarak Malik10Abd El-Zaher M. A. Mustafa11Baber Ali12Department of Botany, Lahore College for Women UniversityDepartment of Botany, Lahore College for Women UniversityDepartment of Horticulture, Faculty of Agricultural Sciences, University of the PunjabSchool of Biological Sciences, University of the PunjabDepartment of Horticulture, Faculty of Agricultural Sciences, University of the PunjabDepartment of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the PunjabDepartment of Botany, Lahore College for Women UniversityDepartment of Botany, Lahore College for Women UniversityCollege of Plant Science and Technology, Huazhong Agricultural UniversityDepartment of Horticulture, Faculty of Agricultural Sciences, University of the PunjabDepartment of Biomedical Sciences, Institute of Health, Jimma UniversityDepartment of Botany and Microbiology, College of Science, King Saud UniversityDepartment of Plant Sciences, Quaid-I-Azam UniversityAbstract 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.https://doi.org/10.1186/s12870-023-04647-4CCO gene familyC. sativusChitosan oligosaccharidesPhloem content |
| spellingShingle | Jannat Akram Riffat Siddique Muhammad Shafiq Bushra Tabassum Muhammad Tariq Manzoor Muhammad Arshad Javed Samia Anwar Bader Un Nisa Muhammad Hamzah Saleem Bilal Javed Tabarak Malik Abd El-Zaher M. A. Mustafa Baber Ali Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana BMC Plant Biology CCO gene family C. sativus Chitosan oligosaccharides Phloem content |
| title | Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana |
| title_full | Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana |
| title_fullStr | Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana |
| title_full_unstemmed | Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana |
| title_short | Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana |
| title_sort | genome wide identification of cco gene family in cucumber cucumis sativus and its comparative analysis with a thaliana |
| topic | CCO gene family C. sativus Chitosan oligosaccharides Phloem content |
| url | https://doi.org/10.1186/s12870-023-04647-4 |
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