Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution
In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and in...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1179009/full |
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| author | Xiaomin Wang Xiaomin Wang Xiaomin Wang Shengyi Bai Zhaolei Zhang Fushun Zheng Lina Song Lu Wen Meng Guo Meng Guo Meng Guo Guoxin Cheng Guoxin Cheng Guoxin Cheng Wenkong Yao Wenkong Yao Wenkong Yao Yanming Gao Yanming Gao Yanming Gao Jianshe Li Jianshe Li Jianshe Li |
| author_facet | Xiaomin Wang Xiaomin Wang Xiaomin Wang Shengyi Bai Zhaolei Zhang Fushun Zheng Lina Song Lu Wen Meng Guo Meng Guo Meng Guo Guoxin Cheng Guoxin Cheng Guoxin Cheng Wenkong Yao Wenkong Yao Wenkong Yao Yanming Gao Yanming Gao Yanming Gao Jianshe Li Jianshe Li Jianshe Li |
| author_sort | Xiaomin Wang |
| collection | DOAJ |
| description | In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average KA/KS ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato. |
| first_indexed | 2024-04-09T13:45:03Z |
| format | Article |
| id | doaj.art-dd3796f04eda4d5a84fa9686ed25cadc |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T13:45:03Z |
| publishDate | 2023-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-dd3796f04eda4d5a84fa9686ed25cadc2023-05-09T05:19:50ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-05-011410.3389/fpls.2023.11790091179009Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolutionXiaomin Wang0Xiaomin Wang1Xiaomin Wang2Shengyi Bai3Zhaolei Zhang4Fushun Zheng5Lina Song6Lu Wen7Meng Guo8Meng Guo9Meng Guo10Guoxin Cheng11Guoxin Cheng12Guoxin Cheng13Wenkong Yao14Wenkong Yao15Wenkong Yao16Yanming Gao17Yanming Gao18Yanming Gao19Jianshe Li20Jianshe Li21Jianshe Li22College of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaNingxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, ChinaKey Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaHebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaNingxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, ChinaKey Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaNingxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, ChinaKey Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaNingxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, ChinaKey Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaNingxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, ChinaKey Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, ChinaCollege of Enology and Horticultrue, Ningxia University, Yinchuan, ChinaNingxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, ChinaKey Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, ChinaIn order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average KA/KS ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.https://www.frontiersin.org/articles/10.3389/fpls.2023.1179009/fulltomatogermplasmchloroplast genomephylogeneticadaptive evolution |
| spellingShingle | Xiaomin Wang Xiaomin Wang Xiaomin Wang Shengyi Bai Zhaolei Zhang Fushun Zheng Lina Song Lu Wen Meng Guo Meng Guo Meng Guo Guoxin Cheng Guoxin Cheng Guoxin Cheng Wenkong Yao Wenkong Yao Wenkong Yao Yanming Gao Yanming Gao Yanming Gao Jianshe Li Jianshe Li Jianshe Li Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution Frontiers in Plant Science tomato germplasm chloroplast genome phylogenetic adaptive evolution |
| title | Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution |
| title_full | Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution |
| title_fullStr | Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution |
| title_full_unstemmed | Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution |
| title_short | Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution |
| title_sort | comparative analysis of chloroplast genomes of 29 tomato germplasms genome structures phylogenetic relationships and adaptive evolution |
| topic | tomato germplasm chloroplast genome phylogenetic adaptive evolution |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1179009/full |
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