Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae)
Abstract Background The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure and evolutionary history of the genus remain poorly understood. In this study, we comprehensively...
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2024-12-01
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| Online Access: | https://doi.org/10.1186/s12870-024-05874-z |
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| author | Lifang Yang Shoujun Zhang Chunya Wu Xiaolong Jiang Min Deng |
| author_facet | Lifang Yang Shoujun Zhang Chunya Wu Xiaolong Jiang Min Deng |
| author_sort | Lifang Yang |
| collection | DOAJ |
| description | Abstract Background The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure and evolutionary history of the genus remain poorly understood. In this study, we comprehensively analyzed the 34 plastomes representing 33 Lithocarpus species. Of which, 21 were newly assembled. The plastome-based phylogenomic tree was reconstructed to reveal the maternal evolutionary patterns of the genus. Results The Lithocarpus plastomes exhibit a typical quadripartite structure, ranging in length from 161,010 to 161,476 bp, and containing 131 genes, including 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Remarkably, the infA gene was identified as a pseudogene in 17 species. Significant variability was observed in simple sequence repeats (SSRs) as well as in the boundary regions between the two single-copy regions and the inverted repeat region (SC/IR) across the plastomes. Additionally, four genes (accD, atpF, rpl32, and rps8) were found to be under positive selection. The monophyletic status of Lithocarpus was strongly supported by plastome-based phylogeny; however, the phylogenetic tree topology showed a significant difference from that obtained by the nuclear genome-based phylogeny. Conclusions The plastome of Fagaceae is generally conserved. Nevertheless, genes related to metabolism, photosynthesis, and energy were under strong positive selection in Lithocarpus, likely driven by environmental pressures and local adaptation. The plastome-based phylogeny confirmed the monophyletic status of Lithocarpus and revealed a phylogeographic pattern indicating limited seed-mediated gene flow in the ancestral lineage. The prevalence of cytonuclear discordance in Lithocarpus and other Fagaceae genera suggests that ancient introgression, incomplete lineage sorting, and asymmetrical seed- and pollen-mediated geneflow might contribute to this discordance. Future studies are essential to test these hypotheses and further elucidate the divergence patterns of this unique Asian evergreen lineage. |
| format | Article |
| id | doaj-art-da27de03cc5a4d6dbad6cbbea9b36438 |
| institution | OA Journals |
| issn | 1471-2229 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-da27de03cc5a4d6dbad6cbbea9b364382025-08-20T01:47:55ZengBMCBMC Plant Biology1471-22292024-12-0124111910.1186/s12870-024-05874-zPlastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae)Lifang Yang0Shoujun Zhang1Chunya Wu2Xiaolong Jiang3Min Deng4Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan UniversityCenter for Horticulture and Conservation, Wuhan Botanical Garden, Chinese Academy of SciencesYunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan UniversityCollege of Forestry, Central South University of Forestry and TechnologyYunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan UniversityAbstract Background The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure and evolutionary history of the genus remain poorly understood. In this study, we comprehensively analyzed the 34 plastomes representing 33 Lithocarpus species. Of which, 21 were newly assembled. The plastome-based phylogenomic tree was reconstructed to reveal the maternal evolutionary patterns of the genus. Results The Lithocarpus plastomes exhibit a typical quadripartite structure, ranging in length from 161,010 to 161,476 bp, and containing 131 genes, including 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Remarkably, the infA gene was identified as a pseudogene in 17 species. Significant variability was observed in simple sequence repeats (SSRs) as well as in the boundary regions between the two single-copy regions and the inverted repeat region (SC/IR) across the plastomes. Additionally, four genes (accD, atpF, rpl32, and rps8) were found to be under positive selection. The monophyletic status of Lithocarpus was strongly supported by plastome-based phylogeny; however, the phylogenetic tree topology showed a significant difference from that obtained by the nuclear genome-based phylogeny. Conclusions The plastome of Fagaceae is generally conserved. Nevertheless, genes related to metabolism, photosynthesis, and energy were under strong positive selection in Lithocarpus, likely driven by environmental pressures and local adaptation. The plastome-based phylogeny confirmed the monophyletic status of Lithocarpus and revealed a phylogeographic pattern indicating limited seed-mediated gene flow in the ancestral lineage. The prevalence of cytonuclear discordance in Lithocarpus and other Fagaceae genera suggests that ancient introgression, incomplete lineage sorting, and asymmetrical seed- and pollen-mediated geneflow might contribute to this discordance. Future studies are essential to test these hypotheses and further elucidate the divergence patterns of this unique Asian evergreen lineage.https://doi.org/10.1186/s12870-024-05874-zPhylogenomicsPlastomeEvolutionPositive selection |
| spellingShingle | Lifang Yang Shoujun Zhang Chunya Wu Xiaolong Jiang Min Deng Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae) BMC Plant Biology Phylogenomics Plastome Evolution Positive selection |
| title | Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae) |
| title_full | Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae) |
| title_fullStr | Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae) |
| title_full_unstemmed | Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae) |
| title_short | Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae) |
| title_sort | plastome characterization and its phylogenetic implications on lithocarpus fagaceae |
| topic | Phylogenomics Plastome Evolution Positive selection |
| url | https://doi.org/10.1186/s12870-024-05874-z |
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