Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus
Abstract Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and comp...
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| Format: | Article |
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Wiley
2021-10-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.8063 |
| _version_ | 1818558827077828608 |
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| author | Xuan Li Yongfu Li Steven Paul Sylvester Mingyue Zang Yousry A. El‐Kassaby Yanming Fang |
| author_facet | Xuan Li Yongfu Li Steven Paul Sylvester Mingyue Zang Yousry A. El‐Kassaby Yanming Fang |
| author_sort | Xuan Li |
| collection | DOAJ |
| description | Abstract Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein‐coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein‐coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH‐psbA, trnK_UUU‐rps16, trnfM_CAU‐rps14, trnS_GCU‐trnG_GCC, and atpF‐atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear. |
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| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-14T00:17:22Z |
| publishDate | 2021-10-01 |
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| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-6c67cb5f86ea4b5aa65c17898136b0ba2022-12-21T23:25:26ZengWileyEcology and Evolution2045-77582021-10-011119134011341410.1002/ece3.8063Evolutionary patterns of nucleotide substitution rates in plastid genomes of QuercusXuan Li0Yongfu Li1Steven Paul Sylvester2Mingyue Zang3Yousry A. El‐Kassaby4Yanming Fang5Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing ChinaKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing ChinaKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing ChinaKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing ChinaDepartment of Forest and Conservation Sciences Faculty of Forestry The University of British Columbia Vancouver BC CanadaKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation College of Biology and the Environment Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing ChinaAbstract Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein‐coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein‐coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH‐psbA, trnK_UUU‐rps16, trnfM_CAU‐rps14, trnS_GCU‐trnG_GCC, and atpF‐atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.https://doi.org/10.1002/ece3.8063chloroplast genomeevolutionary ratenonsynonymous substitutionoaksselective pressuresynonymous substitution |
| spellingShingle | Xuan Li Yongfu Li Steven Paul Sylvester Mingyue Zang Yousry A. El‐Kassaby Yanming Fang Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus Ecology and Evolution chloroplast genome evolutionary rate nonsynonymous substitution oaks selective pressure synonymous substitution |
| title | Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus |
| title_full | Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus |
| title_fullStr | Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus |
| title_full_unstemmed | Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus |
| title_short | Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus |
| title_sort | evolutionary patterns of nucleotide substitution rates in plastid genomes of quercus |
| topic | chloroplast genome evolutionary rate nonsynonymous substitution oaks selective pressure synonymous substitution |
| url | https://doi.org/10.1002/ece3.8063 |
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