Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress
The <i>Citrus clementina</i> (citrus) plant produces various phytohormones due to the significant involvement of the carotenoid cleavage oxygenase (<i>CCO</i>) gene family in its growth and development. <i>CCO</i> genes can be divided into two main categories: <...
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2025-01-01
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| author | Sadaf Sarwar Adnan Sami Muhammad Zeshan Haider Layba Tasawar Jannat Akram Arsalan Ahmad Muhammad Shafiq Haitham E. M. Zaki Gabrijel Ondrasek Muhammad Shafiq Shahid |
| author_facet | Sadaf Sarwar Adnan Sami Muhammad Zeshan Haider Layba Tasawar Jannat Akram Arsalan Ahmad Muhammad Shafiq Haitham E. M. Zaki Gabrijel Ondrasek Muhammad Shafiq Shahid |
| author_sort | Sadaf Sarwar |
| collection | DOAJ |
| description | The <i>Citrus clementina</i> (citrus) plant produces various phytohormones due to the significant involvement of the carotenoid cleavage oxygenase (<i>CCO</i>) gene family in its growth and development. <i>CCO</i> genes can be divided into two main categories: <i>NCED</i> (9-cis-epoxy carotenoid dioxygenase), responsible for abscisic acid (ABA) production, and <i>CCD</i> (carotenoid cleavage dioxygenase), involved in pigment and strigolactone formation. To better understand the roles and positions of <i>CcCCO</i> gene members in relation to these hormones, researchers analyzed the clementine genome. To identify their structural features, they employed phylogenetic analysis, protein interactions, localization, structure, miRNA targets, evolutionary analysis, and transcriptome studies. The study revealed the presence of 15 <i>CcCCO</i> genes, including 11 <i>NCED</i> and 4 <i>CCD</i> genes, scattered across various chromosomes, with the majority located in chloroplasts. Promoter sequencing analysis indicated the presence of different cis-regulatory elements that likely interacted with phytohormones, such as auxin and abscisic acid among others. Notably, two genes, <i>CcNCED1</i> and <i>CcNCED3</i>, were significantly expressed among the <i>CCO</i> genes, and these were found to be expressed during stress and played a crucial role in enabling optimal plant development. Furthermore, a comprehensive genome-wide comparison of <i>CCO</i> genes in <i>C. Clementine</i> and <i>Arabidopsis thaliana</i> models was conducted to understand their functional characteristics. This research provides a solid foundation for further exploration of the unique attributes of the <i>C. clementina</i> plant, contributing to a deeper understanding of its growth and development processes. |
| format | Article |
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| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-cf9e376bf2334b8c975d2468420669882025-01-24T13:46:56ZengMDPI AGPlants2223-77472025-01-0114224910.3390/plants14020249Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic StressSadaf Sarwar0Adnan Sami1Muhammad Zeshan Haider2Layba Tasawar3Jannat Akram4Arsalan Ahmad5Muhammad Shafiq6Haitham E. M. Zaki7Gabrijel Ondrasek8Muhammad Shafiq Shahid9Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanDepartment of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanDepartment of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanDepartment of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanDepartment of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanDepartment of Entomology, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanDepartment of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore P.O. Box 54590, PakistanHorticulture Department, Faculty of Agriculture, Minia University, Minya 61517, EgyptFaculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, CroatiaDepartment of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat 123, OmanThe <i>Citrus clementina</i> (citrus) plant produces various phytohormones due to the significant involvement of the carotenoid cleavage oxygenase (<i>CCO</i>) gene family in its growth and development. <i>CCO</i> genes can be divided into two main categories: <i>NCED</i> (9-cis-epoxy carotenoid dioxygenase), responsible for abscisic acid (ABA) production, and <i>CCD</i> (carotenoid cleavage dioxygenase), involved in pigment and strigolactone formation. To better understand the roles and positions of <i>CcCCO</i> gene members in relation to these hormones, researchers analyzed the clementine genome. To identify their structural features, they employed phylogenetic analysis, protein interactions, localization, structure, miRNA targets, evolutionary analysis, and transcriptome studies. The study revealed the presence of 15 <i>CcCCO</i> genes, including 11 <i>NCED</i> and 4 <i>CCD</i> genes, scattered across various chromosomes, with the majority located in chloroplasts. Promoter sequencing analysis indicated the presence of different cis-regulatory elements that likely interacted with phytohormones, such as auxin and abscisic acid among others. Notably, two genes, <i>CcNCED1</i> and <i>CcNCED3</i>, were significantly expressed among the <i>CCO</i> genes, and these were found to be expressed during stress and played a crucial role in enabling optimal plant development. Furthermore, a comprehensive genome-wide comparison of <i>CCO</i> genes in <i>C. Clementine</i> and <i>Arabidopsis thaliana</i> models was conducted to understand their functional characteristics. This research provides a solid foundation for further exploration of the unique attributes of the <i>C. clementina</i> plant, contributing to a deeper understanding of its growth and development processes.https://www.mdpi.com/2223-7747/14/2/249carotenoid cleavage oxygenase (CCO)phytohormonesgene expressionstress responsegenome-wide analysis |
| spellingShingle | Sadaf Sarwar Adnan Sami Muhammad Zeshan Haider Layba Tasawar Jannat Akram Arsalan Ahmad Muhammad Shafiq Haitham E. M. Zaki Gabrijel Ondrasek Muhammad Shafiq Shahid Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress Plants carotenoid cleavage oxygenase (CCO) phytohormones gene expression stress response genome-wide analysis |
| title | Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress |
| title_full | Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress |
| title_fullStr | Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress |
| title_full_unstemmed | Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress |
| title_short | Genome-Wide Identification and In Silico Expression Analysis of <i>CCO</i> Gene Family in <i>Citrus clementina</i> (Citrus) in Response to Abiotic Stress |
| title_sort | genome wide identification and in silico expression analysis of i cco i gene family in i citrus clementina i citrus in response to abiotic stress |
| topic | carotenoid cleavage oxygenase (CCO) phytohormones gene expression stress response genome-wide analysis |
| url | https://www.mdpi.com/2223-7747/14/2/249 |
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