Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato
NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (<i>S. lycopersicum</i>) and 88 (<i>S. pen...
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MDPI AG
2022-08-01
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| author | Jiale Yuan Ying Liu Zhenyi Wang Tianyu Lei Yanfang Hu Lan Zhang Min Yuan Jinpeng Wang Yuxian Li |
| author_facet | Jiale Yuan Ying Liu Zhenyi Wang Tianyu Lei Yanfang Hu Lan Zhang Min Yuan Jinpeng Wang Yuxian Li |
| author_sort | Jiale Yuan |
| collection | DOAJ |
| description | NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (<i>S. lycopersicum</i>) and 88 (<i>S. pennellii</i>) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived <i>NAC</i> genes had more rearrangement events, so it was different from the DWGT-derived <i>NAC</i> genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived <i>NAC</i> genes tended to be positively selected in <i>S. lycopersicum</i> and negatively selected in <i>S. pennellii</i>. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived <i>NAC</i> genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived <i>NAC</i> genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained <i>NAC</i> genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants. |
| first_indexed | 2024-03-09T09:53:58Z |
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| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T09:53:58Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-887ccb806ebb4a7087cca1ffe2f998d82023-12-01T23:54:41ZengMDPI AGLife2075-17292022-08-01128123610.3390/life12081236Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the TomatoJiale Yuan0Ying Liu1Zhenyi Wang2Tianyu Lei3Yanfang Hu4Lan Zhang5Min Yuan6Jinpeng Wang7Yuxian Li8Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaCenter for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan 063000, ChinaNAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (<i>S. lycopersicum</i>) and 88 (<i>S. pennellii</i>) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived <i>NAC</i> genes had more rearrangement events, so it was different from the DWGT-derived <i>NAC</i> genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived <i>NAC</i> genes tended to be positively selected in <i>S. lycopersicum</i> and negatively selected in <i>S. pennellii</i>. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived <i>NAC</i> genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived <i>NAC</i> genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained <i>NAC</i> genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants.https://www.mdpi.com/2075-1729/12/8/1236paleohexaploidizationtomatoNAC transcription factorfruit ripening |
| spellingShingle | Jiale Yuan Ying Liu Zhenyi Wang Tianyu Lei Yanfang Hu Lan Zhang Min Yuan Jinpeng Wang Yuxian Li Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato Life paleohexaploidization tomato NAC transcription factor fruit ripening |
| title | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
| title_full | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
| title_fullStr | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
| title_full_unstemmed | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
| title_short | Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato |
| title_sort | genome wide analysis of the nac family associated with two paleohexaploidization events in the tomato |
| topic | paleohexaploidization tomato NAC transcription factor fruit ripening |
| url | https://www.mdpi.com/2075-1729/12/8/1236 |
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