Abstract
Green plants and algae have plastids of which chloroplasts are most common. Chloroplasts contain their own genomes, which are relatively stable. Approximately 120 genes are in plastomes and mostly encode proteins used in photosynthesis, protein synthesis, and DNA replication. They provide valuable resources to study the plastogenomics, which helps in understanding the process of evolution in one of the oldest living plants and their interrelationship with angiosperms. Comparing the components of plastomes with those of whole genomes or proteome sequences provides important insights into plant phylogeny and evolution. In the recent years, phylogenomics based on chloroplast genomes has demonstrated numerous advantages in plant phylogenetics. Chloroplast phylogenomics can provide a framework for assessing the impact of reticulate evolution in the early evolution of ferns, especially now the more nuclear data is becoming available. In this review, an attempt is made to study plastid genomes and comparisons of gene content, gene arrangement, gene expression, and gene sequences between extant among various fern species.
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Acknowledgments
This chapter is dedicated to my (AK) teacher Dr. K. K. Sharma for introducing the subject of pteridophytes now “monilophytes” during master’s study at the University of Rajasthan, Jaipur. We are also thankful to Professor S.K. Verma and Professor S.P. Khullar noted pteridologists for the support and during the preparation of this MS. Authors acknowledge with thanks the authors of publications quoted here:
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Table 4.1: Rothfels, C.J., et al. (2015). The evolutionary history of ferns inferred from 25 low-copy nuclear genes. American Journal of Botany, 102: 1089-1107. https://doi.org/10.3732/ajb.1500089. Reproduced with license number 5087470694801 dated 14 June 2021.
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Figure 4.1: Lu, J.-M. et al. (2015). Chloroplast phylogenomics resolves key relationships in ferns. Jnl of Systematics Evolution, 53: 448–457. https://doi.org/10.1111/jse.12180. Reproduced with license number 5085221071437 dated 10 June 2021
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Figure 4.2: Shim, Hyeonah et al. (2021) “Plastid Genomes of the Early Vascular Plant Genus Selaginella Have Unusual Direct Repeat Structures and Drastically Reduced Gene Numbers” Int. J. Mol. Sci. 22, no. 2: 641. https://doi.org/10.3390/ijms22020641. An open-access article distributed under the terms of the Creative Commons CC BY license
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Figure 4.3: Grewe et al. (2013). Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes. BMC Evol Biol 13, 8. https://doi.org/10.1186/1471-2148-13-8
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Figure 4.4: Fan R, Ma W, Liu S, Huang Q. Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis. Ecol Evol. 2021 Mar 18;11(9):4550–4563. doi: https://doi.org/10.1002/ece3.7350. PMID: 33976830; PMCID: PMC8093657
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Figure 4.5: Fan R, Ma W, Liu S, Huang Q. Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis. Ecol Evol. 2021 Mar 18;11(9):4550–4563. doi: https://doi.org/10.1002/ece3.7350. This is an open-access article distributed under the terms of the Creative Commons CC BY license
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Figure 4.6: Li, FW., Brouwer, P., Carretero-Paulet, L. et al. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 4, 460–472 (2018). https://doi.org/10.1038/s41477-018-0188-8. This is an open-access article distributed under the terms of the Creative Commons CC BY license
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Figure 4.7: Liu S, et al. (2021). Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences. BMC Plant Biol. 2021 Jan 7;21(1):31. doi: https://doi.org/10.1186/s12870-020-02800-x. This article is licensed under a Creative Commons Attribution 4.0 International License. http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain
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Figure 4.8: Xu, L., Xing, Y., Wang, B. et al. Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. Chin Med 14, 9 (2019). https://doi.org/10.1186/s13020-019-0230-4. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)
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Figure 4.9: Liu et al. (2021). Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences. BMC Plant Biol 21, 31 (2021). The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/)
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Figure 4.10: Li, F. W., Kuo, L. Y., Pryer, K. M., & Rothfels, C. J. (2016). Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content. Genome biology and evolution, 8(8), 2452–2458. https://doi.org/10.1093/gbe/evw167. Reproduced with license number 5101790146234 dated 4 July 2021
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Figure 4.11: Liu et al. (2020) depicted sizes of each part of 16 fern complete plastome sequences. Liu, S., Wang, Z., Wang, H. et al. Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns. Sci Rep 10, 9394 (2020). https://doi.org/10.1038/s41598-020-66219-y. This is an open-access article distributed under the terms of the Creative Commons CC BY license
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Figure 4.12: Liu, S., Wang, Z., Wang, H. et al. (2020). Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns. Sci Rep 10, 9394. https://doi.org/10.1038/s41598-020-66219-y. This is an open-access article distributed under the terms of the Creative Commons CC BY license
AK is thankful to his wife Professor Dr. Vijay Rani Kumar Retd Professor of Botany for critically examining the MS and valuable suggestions.
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Kumar, A., Giri, P., Uniyal, P.L. (2022). Plastogenomics Provides a Tool to Study Phylogenetic Interrelationships of Monilophytes: A Review. In: Marimuthu, J., Fernández, H., Kumar, A., Thangaiah, S. (eds) Ferns. Springer, Singapore. https://doi.org/10.1007/978-981-16-6170-9_4
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