Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm
IntroductionGaruga forrestii W. W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This species plays a crucial role in maintaining biodiversity in these ecosystems.MethodsWe performed de novo assembly of the Garuga forrestii mitochondrial genome usi...
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Frontiers Media S.A.
2025-01-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1509669/full |
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| author | Rong Chen Rong Chen Rong Chen Rong Chen Rui Rao Rui Rao Rui Rao Rui Rao Chun Wang Chun Wang Chun Wang Chun Wang Dongbo Zhu Dongbo Zhu Dongbo Zhu Dongbo Zhu Fen Yuan Fen Yuan Fen Yuan Fen Yuan Liangliang Yue Liangliang Yue Liangliang Yue Liangliang Yue |
| author_facet | Rong Chen Rong Chen Rong Chen Rong Chen Rui Rao Rui Rao Rui Rao Rui Rao Chun Wang Chun Wang Chun Wang Chun Wang Dongbo Zhu Dongbo Zhu Dongbo Zhu Dongbo Zhu Fen Yuan Fen Yuan Fen Yuan Fen Yuan Liangliang Yue Liangliang Yue Liangliang Yue Liangliang Yue |
| author_sort | Rong Chen |
| collection | DOAJ |
| description | IntroductionGaruga forrestii W. W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This species plays a crucial role in maintaining biodiversity in these ecosystems.MethodsWe performed de novo assembly of the Garuga forrestii mitochondrial genome using PMAT (v.1.5.4), resulting in a typical circular molecule of 606,853 bp. The genome consists of 31 tRNA genes, 3 rRNA genes, 35 protein-coding genes, and 1 pseudogene. The study also investigates RNA editing sites and evolutionary patterns.ResultsThe mitochondrial genome exhibits a low proportion of repetitive sequences (3.30%), suggesting a highly conserved structure. A high copy number of the trnM-CAT gene (4 copies) is noted, which may contribute to genomic rearrangement and adaptive evolution. Among the 476 RNA editing sites, hydrophilic-hydrophobic and hydrophobic-hydrophobic editing events are most common, accounting for 77.10%. Negative selection predominates among most genes (Ka/Ks < 1), while a few genes (e.g., matR, nad3, rps1, rps12, and rps4) show signs of positive selection (Ka/Ks > 1), potentially conferring evolutionary advantages. Additionally, a significant A/T bias is observed at the third codon position. Phylogenomic analysis supports the APG IV classification, with no evidence of horizontal gene transfer.DiscussionThis mitochondrial genome offers valuable insights into the adaptive mechanisms and evolutionary processes of Garuga forrestii. It enhances our understanding of the species' biogeography in tropical Southeast Asia and Southwest China, providing key information on the evolutionary history of this genus. |
| format | Article |
| id | doaj-art-ebd4ed255b47449eb70da5ccf4263ff6 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-ebd4ed255b47449eb70da5ccf4263ff62025-01-20T07:20:11ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.15096691509669Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. SmRong Chen0Rong Chen1Rong Chen2Rong Chen3Rui Rao4Rui Rao5Rui Rao6Rui Rao7Chun Wang8Chun Wang9Chun Wang10Chun Wang11Dongbo Zhu12Dongbo Zhu13Dongbo Zhu14Dongbo Zhu15Fen Yuan16Fen Yuan17Fen Yuan18Fen Yuan19Liangliang Yue20Liangliang Yue21Liangliang Yue22Liangliang Yue23Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, ChinaNational Plateau Wetlands Research Center, Southwest Forestry University, Kunming, ChinaNational Wetland Ecosystem Fixed Research Station of Yunnan Dianchi, Southwest Forestry University, Kunming, ChinaDianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Kunming, ChinaYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, ChinaNational Plateau Wetlands Research Center, Southwest Forestry University, Kunming, ChinaNational Wetland Ecosystem Fixed Research Station of Yunnan Dianchi, Southwest Forestry University, Kunming, ChinaDianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Kunming, ChinaYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, ChinaNational Plateau Wetlands Research Center, Southwest Forestry University, Kunming, ChinaNational Wetland Ecosystem Fixed Research Station of Yunnan Dianchi, Southwest Forestry University, Kunming, ChinaDianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Kunming, ChinaYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, ChinaNational Plateau Wetlands Research Center, Southwest Forestry University, Kunming, ChinaNational Wetland Ecosystem Fixed Research Station of Yunnan Dianchi, Southwest Forestry University, Kunming, ChinaDianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Kunming, ChinaYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, ChinaNational Plateau Wetlands Research Center, Southwest Forestry University, Kunming, ChinaNational Wetland Ecosystem Fixed Research Station of Yunnan Dianchi, Southwest Forestry University, Kunming, ChinaDianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Kunming, ChinaYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming, ChinaNational Plateau Wetlands Research Center, Southwest Forestry University, Kunming, ChinaNational Wetland Ecosystem Fixed Research Station of Yunnan Dianchi, Southwest Forestry University, Kunming, ChinaDianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Kunming, ChinaIntroductionGaruga forrestii W. W. Sm. is a tree species of the Burseraceae family, endemic to China, found in hot/warm-dry valleys. This species plays a crucial role in maintaining biodiversity in these ecosystems.MethodsWe performed de novo assembly of the Garuga forrestii mitochondrial genome using PMAT (v.1.5.4), resulting in a typical circular molecule of 606,853 bp. The genome consists of 31 tRNA genes, 3 rRNA genes, 35 protein-coding genes, and 1 pseudogene. The study also investigates RNA editing sites and evolutionary patterns.ResultsThe mitochondrial genome exhibits a low proportion of repetitive sequences (3.30%), suggesting a highly conserved structure. A high copy number of the trnM-CAT gene (4 copies) is noted, which may contribute to genomic rearrangement and adaptive evolution. Among the 476 RNA editing sites, hydrophilic-hydrophobic and hydrophobic-hydrophobic editing events are most common, accounting for 77.10%. Negative selection predominates among most genes (Ka/Ks < 1), while a few genes (e.g., matR, nad3, rps1, rps12, and rps4) show signs of positive selection (Ka/Ks > 1), potentially conferring evolutionary advantages. Additionally, a significant A/T bias is observed at the third codon position. Phylogenomic analysis supports the APG IV classification, with no evidence of horizontal gene transfer.DiscussionThis mitochondrial genome offers valuable insights into the adaptive mechanisms and evolutionary processes of Garuga forrestii. It enhances our understanding of the species' biogeography in tropical Southeast Asia and Southwest China, providing key information on the evolutionary history of this genus.https://www.frontiersin.org/articles/10.3389/fpls.2024.1509669/fullGaruga forrestiimitochondrial genomephylogenomicadaptationrepetitive sequence |
| spellingShingle | Rong Chen Rong Chen Rong Chen Rong Chen Rui Rao Rui Rao Rui Rao Rui Rao Chun Wang Chun Wang Chun Wang Chun Wang Dongbo Zhu Dongbo Zhu Dongbo Zhu Dongbo Zhu Fen Yuan Fen Yuan Fen Yuan Fen Yuan Liangliang Yue Liangliang Yue Liangliang Yue Liangliang Yue Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm Frontiers in Plant Science Garuga forrestii mitochondrial genome phylogenomic adaptation repetitive sequence |
| title | Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm |
| title_full | Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm |
| title_fullStr | Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm |
| title_full_unstemmed | Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm |
| title_short | Features and evolutionary adaptations of the mitochondrial genome of Garuga forrestii W. W. Sm |
| title_sort | features and evolutionary adaptations of the mitochondrial genome of garuga forrestii w w sm |
| topic | Garuga forrestii mitochondrial genome phylogenomic adaptation repetitive sequence |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1509669/full |
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