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Celep, F., Kahraman, A., Guerin, G. R., Karabacak, E., Akaydın, G., & Doğan, M. (2022). Nutlet micromorphology and its taxonomic and phylogenetic significance in Salvia (Lamiaceae). Plant Biosystems, 156(1), 271-283. https://doi.org/10.1080/11263504.2020.1852331
Chen, Z., Yu, X., Yang, Y., Wei, P., Zhang, W., Li, X., Liu, C.; Zhao, S.; Li, X.; & Liu, X. (2022). Comparative analysis of chloroplast genomes within Saxifraga (Saxifragaceae) takes insights into their genomic evolution and adaption to the high-elevation environment. Genes, 13(9), 1673. https://doi.org/10.3390/genes13091673
Cui, L., Leebens-Mack, J., Wang, L. S., Tang, J., Rymarquis, L., Stern, D. B., & DePamphilis, C. W. (2006). Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach. BMC Evolutionary Biology, 6, 1-12. https://doi.org/10.1186/1471-2148-6-13
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Daniell, H., Jin, S., Zhu, X.-G., Gitzendanner, M. A., Soltis, D. E., & Soltis, P. S. (2021) Green giant a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. Plant Biotechnology Journal, 19(3), 430-447. https:// doi.org/ 10.1111 /pbi.13556
De Las Rivas, J., Lozano, J. J., & Ortiz, A. R. (2002). Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Research, 12(4), 567-583. https://doi.org/10.1101/gr.209402
Dobrogojski, J., Adamiec, M., & Luciński, R. (2020). The chloroplast genome: a review. Acta Physiologiae Plantarum, 42(6), 98. https://doi.org/10.1007/s11738-020-03089-x
Du, Q., Yang, H., Zeng, J., Chen, Z., Zhou, J., Sun, S., Wang, B., & Liu, C. (2022). Comparative genomics and phylogenetic analysis of the chloroplast genomes in three medicinal Salvia species for bioexploration. International Journal of Molecular Sciences, 23(20), 12080. https://doi.org/10.3390/ijms232012080
Foyer, C. H., Noctor, G., & Hodges, M. (2011). Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency. Journal of Experimental Botany, 62(4), 1467-1482. https://doi.org/10.1093/jxb/erq453
Gao, L. Z., Liu, Y. L., Zhang, D., Li, W., Gao, J., Liu, Y., Li, K., Shi, C., Zhao, Y., Zhao, Y.J., Jiao, J.Y., Mao, S.Y.,Gao,C.W., & Eichler, E. E. (2019). Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats. Communications Biology, 2(1), 278. https://doi.org/10.1038/s42003-019-0531-2
Géron, A. (2022). Hands-on machine learning with Scikit-Learn, Keras, and TensorFlow. " O'Reilly Media, Inc.".
Gong, L., Ding, X., Guan, W., Zhang, D., Zhang, J., Bai, J., Xu, W., Huang, J., Qiu, X., Zheng, X., Zhang, D.,Li, S., Huang, Z., & Su, H. (2022). Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC Plant Biology, 22(1), 520. https://doi.org/10.1186/s12870-022-03898-x
Grabelnych, O. I., Borovik, O. A., Tauson, E. L., Pobezhimova, T. P., Katyshev, A. I., Pavlovskaya, N. S., Koroleva, N. A., Lyubushkina, I. V.,Bashmakov, V. Y., Popov, V. N., Borovskii, G. B.,& Voinikov, V. K. (2014). Mitochondrial energy-dissipating systems (alternative oxidase, uncoupling proteins, and external NADH dehydrogenase) are involved in development of frost-resistance of winter wheat seedlings. Biochemistry (Moscow), 79, 506-519. https://doi.org/10.1134/S0006297914060030
Gu, X., Zhu, M., Su, Y., & Wang, T. (2022). A large intergenic spacer leads to the increase in genome size and sequential gene movement around IR/SC boundaries in the chloroplast genome of Adiantum malesianum (Pteridaceae). International Journal of Molecular Sciences, 23(24), 15616. https://doi.org/10.3390/ijms232415616
Guo, Y. Y., Yang, J. X., Bai, M. Z., Zhang, G. Q., & Liu, Z. J. (2021). The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions. BMC Plant Biology, 21(1), 248. https://doi.org/10.1186/s12870-021-03053-y
Hao, J., Liang, Y., Ping, J., Wang, T., & Su, Y. (2024). Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns. Plant Molecular Biology, 114(2), 31. https://doi.org/10.1007/s11103-024-01423-2
Hetland, M. L., & Nelli, F. (2024). Activity 1: Data Analysis with Pandas, Matplotlib, and Seaborn. In Beginning Python: From Novice to Professional (pp. 487-504). Berkeley, CA: Apress. https://doi.org/10.1007/979-8-8688-0196-9_25
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Jackson, H. O., Taunt, H. N., Mordaka, P. M., Smith, A. G., & Purton, S. (2021). The algal chloroplast as a testbed for synthetic biology designs aimed at radically rewiring plant metabolism. Frontiers in Plant Science, 12, 708370. https://doi.org/10.3389/fpls.2021.708370
Jiang, D., Cai, X., Gong, M., Xia, M., Xing, H., Dong, S., Tian, S., Li, J., Lin, J., Liu, Y., & Li, H. L. (2023). Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae). BMC genomics, 24(1), 30. https://doi.org/10.1186/s12864-023-09115-9
Kim, M., Lee, S., Ok, J., Han, B., & Cho, M. (2022, October). Towards sequence-level training for visual tracking. In European Conference on Computer Vision (pp. 534-551). Cham: Springer Nature Switzerland. https://doi.org/10.1007/978-3-031-20047-2_31
Lang, C., Weber, N., Moeller, M., Schramm, L., Schelm, S., Kohlbacher, O., & Fischer, M. (2021). Genetic authentication: Differentiation of hazelnut cultivars using polymorphic sites of the chloroplast genome. Food Control, 130, 108344. https://doi.org/10.1016/j.foodcont.2021.108344
Li, J., Fan, R., Xu, J., Hu, L., Su, F., & Hao, C. (2022). Comparative analysis of the chloroplast genomes of eight Piper species and insights into the utilization of structural variation in phylogenetic analysis. Frontiers in Genetics, 13, 925252. https://doi.org/10.3389/fgene.2022.925252
Li, Z., Fan, H., Yang, L., Wang, S., Hong, D., Cui, W., Wang, T., Wei, C., Sun, Y., Wang, K., & Liu, Y. (2024). Multi-omics analysis of the effects of soil amendment on rapeseed (Brassica napus L.) photosynthesis under drip irrigation with brackish water. International Journal of Molecular Sciences, 25(5), 2521. https://doi.org/10.3390/ijms25052521
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Comparative insights into genomic variability and adaptation in the chloroplast genomes of Salvia japonica and Salvia rosmarinus
Chloroplast genomes provide important information about phylogenetics, plant evolution, and adaptive processes. This study examines the chloroplast genomes of Salvia japonica and Salvia rosmarinus. We conducted structural and functional annotations to identify significant variations in gene content and organization. We found that S. rosmarinus has fewer photosystem II (psb) genes and a greater abundance of hypothetical genes (ycf). This may help maintain genomic stability while facilitating species evolution. There are big differences in insertion-deletion events (indels) and single nucleotide polymorphisms (SNPs) in important gene families, like NADH dehydrogenase and ribosomal proteins. We determined this organizational difference by applying Principal Component Analysis (PCA) to the genomes of the two species, which belong to different and distinct gene categories. Sequence alignment revealed gaps and inconsistencies in genes related to RNA polymerase and photosynthesis. The fact that S. japonica and S. rosmarinus have a lot of different genes and may have adapted to live in different environments suggests that they have had different evolutionary paths. These results give us important information about how Salvia species have evolved and give us a way to think about how chloroplast genomes change in different ecological settings. This study provides a basis for understanding the evolution of the chloroplast genome in the genus Salvia. This study has been significant in clarifying the role of photosynthetic and hypothetical genes in controlling environmental responses. Future study must use transcriptome and ecological data to enhance our understanding of the impact of genetic variants on functionality.
This work was not submitted to any other journal in any form, and the results of this study were not used in any animal experiments or human research.
Supporting Institution
The author has not disclosed any funding.
References
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