Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery
Celery (<i>Apium graveolens</i> L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-08-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/16/8986 |
| _version_ | 1797409792089653248 |
|---|---|
| author | Xiaoming Song Nan Li Yingchao Zhang Yi Liang Rong Zhou Tong Yu Shaoqin Shen Shuyan Feng Yu Zhang Xiuqing Li Hao Lin Xiyin Wang |
| author_facet | Xiaoming Song Nan Li Yingchao Zhang Yi Liang Rong Zhou Tong Yu Shaoqin Shen Shuyan Feng Yu Zhang Xiuqing Li Hao Lin Xiyin Wang |
| author_sort | Xiaoming Song |
| collection | DOAJ |
| description | Celery (<i>Apium graveolens</i> L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics analysis, we identified and conducted a comprehensive analysis of chlorophyll and carotenoid-related genes in celery and six representative species. Significantly, different contents and gene expression patterns were found among three celery varieties. In total, 237 and 290 chlorophyll and carotenoid-related genes were identified in seven species. No notable gene expansion of chlorophyll biosynthesis was detected in examined species. However, the gene encoding ζ-carotene desaturase (ZDS) enzyme in carotenoid was expanded in celery. Comparative genomics and RNA-seq analyses revealed 16 and 5 key genes, respectively, regulating chlorophyll and carotenoid. An intriguing finding is that chlorophyll and carotenoid-related genes were coordinately regulated by transcriptional factors, which could be distinctively classified into positive- and negative-regulation groups. Six <i>CONSTANS</i> (<i>CO</i>)-like transcription factors co-regulated chlorophyll and carotenoid-related genes were identified in celery. In conclusion, this study provides new insights into the regulation of chlorophyll and carotenoid by transcription factors. |
| first_indexed | 2024-03-09T04:20:39Z |
| format | Article |
| id | doaj.art-21a2db9e23dd40b0a481cca3de80719d |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T04:20:39Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-21a2db9e23dd40b0a481cca3de80719d2023-12-03T13:47:45ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-08-012316898610.3390/ijms23168986Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in CeleryXiaoming Song0Nan Li1Yingchao Zhang2Yi Liang3Rong Zhou4Tong Yu5Shaoqin Shen6Shuyan Feng7Yu Zhang8Xiuqing Li9Hao Lin10Xiyin Wang11Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaBeijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, ChinaDepartment of Food Science, Aarhus University, 8200 Aarhus, DenmarkCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaFredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, CanadaCenter for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaCenter for Genomics and Bio-Computing, School of Life Sciences, North China University of Science and Technology, Tangshan 063210, ChinaCelery (<i>Apium graveolens</i> L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics analysis, we identified and conducted a comprehensive analysis of chlorophyll and carotenoid-related genes in celery and six representative species. Significantly, different contents and gene expression patterns were found among three celery varieties. In total, 237 and 290 chlorophyll and carotenoid-related genes were identified in seven species. No notable gene expansion of chlorophyll biosynthesis was detected in examined species. However, the gene encoding ζ-carotene desaturase (ZDS) enzyme in carotenoid was expanded in celery. Comparative genomics and RNA-seq analyses revealed 16 and 5 key genes, respectively, regulating chlorophyll and carotenoid. An intriguing finding is that chlorophyll and carotenoid-related genes were coordinately regulated by transcriptional factors, which could be distinctively classified into positive- and negative-regulation groups. Six <i>CONSTANS</i> (<i>CO</i>)-like transcription factors co-regulated chlorophyll and carotenoid-related genes were identified in celery. In conclusion, this study provides new insights into the regulation of chlorophyll and carotenoid by transcription factors.https://www.mdpi.com/1422-0067/23/16/8986celerychlorophyllcarotenoidgene duplicationexpression patternregulatory network |
| spellingShingle | Xiaoming Song Nan Li Yingchao Zhang Yi Liang Rong Zhou Tong Yu Shaoqin Shen Shuyan Feng Yu Zhang Xiuqing Li Hao Lin Xiyin Wang Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery International Journal of Molecular Sciences celery chlorophyll carotenoid gene duplication expression pattern regulatory network |
| title | Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery |
| title_full | Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery |
| title_fullStr | Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery |
| title_full_unstemmed | Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery |
| title_short | Transcriptomics and Genomics Analysis Uncover the Differentially Expressed Chlorophyll and Carotenoid-Related Genes in Celery |
| title_sort | transcriptomics and genomics analysis uncover the differentially expressed chlorophyll and carotenoid related genes in celery |
| topic | celery chlorophyll carotenoid gene duplication expression pattern regulatory network |
| url | https://www.mdpi.com/1422-0067/23/16/8986 |
| work_keys_str_mv | AT xiaomingsong transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT nanli transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT yingchaozhang transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT yiliang transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT rongzhou transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT tongyu transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT shaoqinshen transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT shuyanfeng transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT yuzhang transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT xiuqingli transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT haolin transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery AT xiyinwang transcriptomicsandgenomicsanalysisuncoverthedifferentiallyexpressedchlorophyllandcarotenoidrelatedgenesincelery |