Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’
ATP-binding cassette (ABC) transporters are a large class of superfamily involved in a variety of biological processes with multiple functions, including phytohormone transport, heavy metal ion detoxification, and so on. Anthocyanin pigmentation in grapes is a commercially important feature of this...
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MDPI AG
2023-04-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/9/5/532 |
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| author | Hui Li Yaxin Yang Qianlan Wang Haoran Li Wu Wang Huan Zheng Jianmin Tao |
| author_facet | Hui Li Yaxin Yang Qianlan Wang Haoran Li Wu Wang Huan Zheng Jianmin Tao |
| author_sort | Hui Li |
| collection | DOAJ |
| description | ATP-binding cassette (ABC) transporters are a large class of superfamily involved in a variety of biological processes with multiple functions, including phytohormone transport, heavy metal ion detoxification, and so on. Anthocyanin pigmentation in grapes is a commercially important feature of this superfamily. To elucidate the mechanisms of the VvABC gene at different stages in grape berries, we analyzed and characterized the ABC family in ‘ZhongShan-HongYu’ (ZS-HY) berries using RNA-seq analysis. In this study, a total of 146 VvABC genes were identified by comprehensive bioinformatics analysis, which outlined their gene structure, chromosomal location, conserved domains, phylogenetic relationships, and collinearity analysis. The VvABC family could be divided into eight subfamilies based on the phylogenetic analysis. Fifty-eight VvABC genes were identified from the RNA-seq data, of which 31 belong to the ABCG subfamily, 15 belong to the ABCC subfamily, 8 belong to the ABCB subfamily, 2 belong to the ABCF subfamily, and only 1 belongs to each of the ABCA and ABCD subfamilies. We used qRT-PCR to detect the expression of VvABC genes in different organs and found that it changed significantly in different organs. Phylogenetic analysis showed that genes involved in anthocyanin transport in other species were closely related to members of the ABCC subfamily. Subsequently, analysis of the promoter elements and the protein interactions of the VvABCC genes using RNA-seq was performed. This study has improved our understanding of the functions of the ABC gene family and provided a basis for the role of ABC genes in grape anthocyanin transport. |
| first_indexed | 2024-03-11T03:41:23Z |
| format | Article |
| id | doaj.art-41f62af597d1474689ffc642128167bb |
| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-11T03:41:23Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj.art-41f62af597d1474689ffc642128167bb2023-11-18T01:34:14ZengMDPI AGHorticulturae2311-75242023-04-019553210.3390/horticulturae9050532Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’Hui Li0Yaxin Yang1Qianlan Wang2Haoran Li3Wu Wang4Huan Zheng5Jianmin Tao6College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaATP-binding cassette (ABC) transporters are a large class of superfamily involved in a variety of biological processes with multiple functions, including phytohormone transport, heavy metal ion detoxification, and so on. Anthocyanin pigmentation in grapes is a commercially important feature of this superfamily. To elucidate the mechanisms of the VvABC gene at different stages in grape berries, we analyzed and characterized the ABC family in ‘ZhongShan-HongYu’ (ZS-HY) berries using RNA-seq analysis. In this study, a total of 146 VvABC genes were identified by comprehensive bioinformatics analysis, which outlined their gene structure, chromosomal location, conserved domains, phylogenetic relationships, and collinearity analysis. The VvABC family could be divided into eight subfamilies based on the phylogenetic analysis. Fifty-eight VvABC genes were identified from the RNA-seq data, of which 31 belong to the ABCG subfamily, 15 belong to the ABCC subfamily, 8 belong to the ABCB subfamily, 2 belong to the ABCF subfamily, and only 1 belongs to each of the ABCA and ABCD subfamilies. We used qRT-PCR to detect the expression of VvABC genes in different organs and found that it changed significantly in different organs. Phylogenetic analysis showed that genes involved in anthocyanin transport in other species were closely related to members of the ABCC subfamily. Subsequently, analysis of the promoter elements and the protein interactions of the VvABCC genes using RNA-seq was performed. This study has improved our understanding of the functions of the ABC gene family and provided a basis for the role of ABC genes in grape anthocyanin transport.https://www.mdpi.com/2311-7524/9/5/532genome-wideABCanthocyaninteinturier grapegene family |
| spellingShingle | Hui Li Yaxin Yang Qianlan Wang Haoran Li Wu Wang Huan Zheng Jianmin Tao Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’ Horticulturae genome-wide ABC anthocyanin teinturier grape gene family |
| title | Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’ |
| title_full | Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’ |
| title_fullStr | Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’ |
| title_full_unstemmed | Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’ |
| title_short | Genome-Wide Identification of ATP-Binding Cassette (ABC) Transporter Provides Insight to Genes Related to Anthocyanin Transportation in New Teinturier Grape Germplasm ‘ZhongShan-HongYu’ |
| title_sort | genome wide identification of atp binding cassette abc transporter provides insight to genes related to anthocyanin transportation in new teinturier grape germplasm zhongshan hongyu |
| topic | genome-wide ABC anthocyanin teinturier grape gene family |
| url | https://www.mdpi.com/2311-7524/9/5/532 |
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