Reflecting on the Mutation Rate Variability in Plant Genomes: An In-depth Analysis

Authors

  • Manuela Horvat Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovak Republic Author
  • Valentina Novak Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovak Republic Author
  • Frederik Antunovic Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovak Republic Author
  • Dario Blazevic Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovak Republic Author

DOI:

https://doi.org/10.63995/TZCK7098

Keywords:

Adaptation; Biodiversity; Epigenetics; Genetic diversity; Mutation rates; Plant genomes; Plant breeding; Evolution

Abstract

Mutation rates, which can vary significantly across different plant species and even within the same genome, are influenced by a complex interplay of genetic, environmental, and epigenetic factors. This study integrates recent advancements in genomic sequencing and bioinformatics to analyze these variabilities comprehensively. By examining a diverse range of plant species, the research identifies key patterns and correlations between mutation rates and various phenotypic traits, ecological niches, and evolutionary histories. Additionally, the study explores how these mutation rates impact plant breeding programs, conservation efforts, and biotechnological innovations. Special attention is given to the implications of high and low mutation rates in response to environmental stressors and their role in facilitating rapid adaptation. Through this in-depth analysis, the article aims to provide a deeper understanding of the mechanisms governing mutation rate variability and their broader significance in plant biology. This knowledge is crucial for developing more effective strategies in agriculture, biodiversity conservation, and the sustainable management of plant genetic resources.

Downloads

Download data is not yet available.

References

Xuehui Huang and Bin Han. “Natural variations and genome-wide association studies in crop plants”. In: Annual review of plant biology 65.1 (2014), pp. 531–551. DOI: https://doi.org/10.1146/annurev-arplant-050213-035715

Uffe Hellsten, Kevin M Wright, Jerry Jenkins, Shengqiang Shu, Yaowu Yuan, Susan R Wessler, Jeremy Schmutz, John H Willis, and Daniel S Rokhsar. “Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing”. In: Proceedings of the National Academy of Sciences 110.48 (2013), pp. 19478–19482. DOI: https://doi.org/10.1073/pnas.1319032110

Braulio J Soto-Cerda and Sylvie Cloutier. “Association mapping in plant genomes”. In: Genetic diversity in plants 29.54 (2012), pp. 10–5772.

Manuel André, João Margarida, Heitor Garcia, and Augusto Dante. “Complexities of Blockchain Technology and Distributed Ledger Technologies: A Detailed Inspection”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 2.1 (2021), pp. 164–177. DOI: https://doi.org/10.63995/PMDT9612

Outi Savolainen and Tanja Pyhäjärvi. “Genomic diversity in forest trees”. In: Current opinion in plant biology 10.2 (2007), pp. 162–167. DOI: https://doi.org/10.1016/j.pbi.2007.01.011

AS Dubrovina and KV Kiselev. “Age-associated alterations in the somatic mutation and DNA methylation levels in plants”. In: Plant Biology 18.2 (2016), pp. 185–196. DOI: https://doi.org/10.1111/plb.12375

Małgorzata Cognominal, Krystyna Patronymic, and Agnieszka Wańkowicz. “Evolving Field of Autonomous Mobile Robotics. Technological Advances and Applications”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 2.2 (2021), pp. 189–200.

Barbara A Schaal and Kenneth M Olsen. “Gene genealogies and population variation in plants”. In: Proceedings of the National Academy of Sciences 97.13 (2000), pp. 7024–7029. DOI: https://doi.org/10.1073/pnas.97.13.7024

W John Kress, Douglas E Soltis, Paul J Kersey, Jill L Wegrzyn, James H Leebens-Mack, Morgan R Gostel, Xin Liu, and Pamela S Soltis. “Green plant genomes: What we know in an era of rapidly expanding opportunities”. In: Proceedings of the National Academy of Sciences 119.4 (2022), e2115640118. DOI: https://doi.org/10.1073/pnas.2115640118

Vaishali Katju and Ulfar Bergthorsson. “Old trade, new tricks: insights into the spontaneous mutation process from the partnering of classical mutation accumulation experiments with high-throughput genomic approaches”. In: Genome Biology and Evolution 11.1 (2019), pp. 136–165. DOI: https://doi.org/10.1093/gbe/evy252

AR Leitch and IJ Leitch. “Ecological and genetic factors linked to contrasting genome dynamics in seed plants”. In: New Phytologist 194.3 (2012), pp. 629–646. DOI: https://doi.org/10.1111/j.1469-8137.2012.04105.x

Blenda Johansson, Elvira Eriksson, Nellie Berglund, and Ingrid Lindgren. “Robotic Surgery: Review on Minimally Invasive Techniques”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 2.2 (2021), pp. 201–210.

Antoine Branca, Timothy D Paape, Peng Zhou, Roman Briskine, Andrew D Farmer, Joann Mudge, Arvind K Bharti, Jimmy E Woodward, Gregory D May, Laurent Gentzbittel, et al. “Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula”. In: Proceedings of the National Academy of Sciences 108.42 (2011), E864–E870. DOI: https://doi.org/10.1073/pnas.1104032108

Clémentine Vitte and Jeffrey L Bennetzen. “Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution”. In: Proceedings of the National Academy of Sciences 103.47 (2006), pp. 17638–17643. DOI: https://doi.org/10.1073/pnas.0605618103

Daniel B Sloan, Bengt Oxelman, Anja Rautenberg, and Douglas R Taylor. “Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae”. In: BMC Evolutionary Biology 9 (2009), pp. 1–16. DOI: https://doi.org/10.1186/1471-2148-9-260

Marc Heylen, Patrick Bossuyt, Philippe Provoost, David Borremans, and Christine Rampelberg. “Making Antennas for 6G”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 3.1 (2022), pp. 235–247.

Yuan O Zhu, Mark L Siegal, David W Hall, and Dmitri A Petrov. “Precise estimates of mutation rate and spectrum in yeast”. In: Proceedings of the National Academy of Sciences 111.22 (2014), E2310–E2318. DOI: https://doi.org/10.1073/pnas.1323011111

Mathieu Siol, Stephen I Wright, and Spencer CH Barrett. “The population genomics of plant adaptation”. In: New Phytologist 188.2 (2010), pp. 313–332. DOI: https://doi.org/10.1111/j.1469-8137.2010.03401.x

Way Sung, Matthew S Ackerman, Samuel F Miller, Thomas G Doak, and Michael Lynch. “Driftbarrier hypothesis and mutation-rate evolution”. In: Proceedings of the National Academy of Sciences 109.45 (2012), pp. 18488–18492. DOI: https://doi.org/10.1073/pnas.1216223109

Valdemar Johansen, Malthe Rasmussen, and Arne Knudsen. “Dielectric Constants and Their Role in Plasma Simulation”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 3.1 (2022), pp. 248–260.

Adriaan Van Der Graaf, René Wardenaar, Drexel A Neumann, Aaron Taudt, Ruth G Shaw, Ritsert C Jansen, Robert J Schmitz, Maria Colomé-Tatché, and Frank Johannes. “Rate, spectrum, and evolutionary dynamics of spontaneous epimutations”. In: Proceedings of the National Academy of Sciences 112.21 (2015), pp. 6676–6681. DOI: https://doi.org/10.1073/pnas.1424254112

Josef Baumgartner, Alexandra Schneider, Ulugbek Zhenis, Franz Jager, and Josef Winkler. “Mastering Neural Network Prediction for Enhanced System Reliability”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 3.1 (2022), pp. 261–274.

Jaume Pellicer, Oriane Hidalgo, Steven Dodsworth, and Ilia J Leitch. “Genome size diversity and its impact on the evolution of land plants”. In: Genes 9.2 (2018), p. 88. DOI: https://doi.org/10.3390/genes9020088

Charles F Baer, Michael M Miyamoto, and Dee R Denver. “Mutation rate variation in multicellular eukaryotes: causes and consequences”. In: Nature Reviews Genetics 8.8 (2007), pp. 619–631. DOI: https://doi.org/10.1038/nrg2158

Jiří Macas, Petr Novák, Jaume Pellicer, Jana Čížková, Andrea Koblížková, Pavel Neumann, Iva Fukova, Jaroslav Doležel, Laura J Kelly, and Ilia J Leitch. “In depth characterization of repetitive DNA in 23 plant genomes reveals sources of genome size variation in the legume tribe Fabeae”. In: PloS one 10.11 (2015), e0143424. DOI: https://doi.org/10.1371/journal.pone.0143424

William Coetzee, Reiner Khumalo, Brendan Le Roux, and Ebrahim Van Wyk. “Sickle Cell Disease: Causes, Symptoms, and Treatment”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 3.1 (2022), pp. 275–286.

Jeffrey D Palmer, Keith L Adams, Yangrae Cho, Christopher L Parkinson, Yin-Long Qiu, and Keming Song. “Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates”. In: Proceedings of the National Academy of Sciences 97.13 (2000), pp. 6960–6966. DOI: https://doi.org/10.1073/pnas.97.13.6960

Nancy A Reichert. “History of plant genetic mutations±human influences”. In: In Vitro Cellular & Developmental Biology-Plant 57.4 (2021), pp. 554–564. DOI: https://doi.org/10.1007/s11627-021-10182-4

Dee R Denver, Peter C Dolan, Larry J Wilhelm, Way Sung, J Ignacio Lucas-Lledó, Dana K Howe, Samantha C Lewis, Kazu Okamoto, W Kelley Thomas, Michael Lynch, et al. “A genomewide view of Caenorhabditis elegans base-substitution mutation processes”. In: Proceedings of the National Academy of Sciences 106.38 (2009), pp. 16310–16314. DOI: https://doi.org/10.1073/pnas.0904895106

Jacob J Michaelson, Yujian Shi, Madhusudan Gujral, Hancheng Zheng, Dheeraj Malhotra, Xin Jin, Minghan Jian, Guangming Liu, Douglas Greer, Abhishek Bhandari, et al. “Whole-genome sequencing in autism identifies hot spots for de novo germline mutation”. In: Cell 151.7 (2012), pp. 1431–1442. DOI: https://doi.org/10.1016/j.cell.2012.11.019

Nima Mostafa, Arman Mohsen, Shahrad Mardin, and Ameen Elyas. “Deciphering the Mysteries: Seasonal Influenza and the Role of Flu Vaccines in Public Health”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 4.1 (2023), pp. 380–392.

Alan F Rubin and Phil Green. “Mutation patterns in cancer genomes”. In: Proceedings of the National Academy of Sciences 106.51 (2009), pp. 21766–21770. DOI: https://doi.org/10.1073/pnas.0912499106

Shira Rubin, Daniel Mizrachi, Noam Friedman, Hila Edri, and Tamar Golan. “The World of Advanced Thin Films: Design, Fabrication, and Applications”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 4.1 (2023), pp. 393–406.

Agnieszka Żmieńko, Anna Samelak, Piotr Kozłowski, and Marek Figlerowicz. “Copy number polymorphism in plant genomes”. In: Theoretical and applied genetics 127 (2014), pp. 1–18. DOI: https://doi.org/10.1007/s00122-013-2177-7

Yangrae Cho, Jeffrey P Mower, Yin-Long Qiu, and Jeffrey D Palmer. “Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants”. In: Proceedings of the National Academy of Sciences 101.51 (2004), pp. 17741–17746. DOI: https://doi.org/10.1073/pnas.0408302101

Paul Gepts. “The contribution of genetic and genomic approaches to plant domestication studies”. In: Current opinion in plant biology 18 (2014), pp. 51–59. DOI: https://doi.org/10.1016/j.pbi.2014.02.001

Kelley Harris. “Evidence for recent, population-specific evolution of the human mutation rate”. In: Proceedings of the National Academy of Sciences 112.11 (2015), pp. 3439–3444. DOI: https://doi.org/10.1073/pnas.1418652112

Fyodor A Kondrashov and Alexey S Kondrashov. “Measurements of spontaneous rates of mutations in the recent past and the near future”. In: Philosophical Transactions of the Royal Society B: Biological Sciences 365.1544 (2010), pp. 1169–1176. DOI: https://doi.org/10.1098/rstb.2009.0286

Detlef Weigel. “Natural variation in Arabidopsis: from molecular genetics to ecological genomics”. In: Plant physiology 158.1 (2012), pp. 2–22. DOI: https://doi.org/10.1104/pp.111.189845

Sean Tan, Wei Lee, Chloe Wong, and Yi Jia Chua. “Exploring the Potential and Advancements of Hydrogen Fuel Cells: Outcomes and Applications”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 4.1 (2023), pp. 407–419.

Caifu Jiang, Aziz Mithani, Eric J Belfield, Richard Mott, Laurence D Hurst, and Nicholas P Harberd. “Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations”. In: Genome research 24.11 (2014), pp. 1821–1829. DOI: https://doi.org/10.1101/gr.177659.114

Haibao Tang, Uzay Sezen, and Andrew H Paterson. “Domestication and plant genomes”. In: Current opinion in plant biology 13.2 (2010), pp. 160–166. DOI: https://doi.org/10.1016/j.pbi.2009.10.008

Jason G Bragg, Megan A Supple, Rose L Andrew, and Justin O Borevitz. “Genomic variation across landscapes: insights and applications”. In: New Phytologist 207.4 (2015), pp. 953–967. DOI: https://doi.org/10.1111/nph.13410

Pádraic J Flood, Jeremy Harbinson, and Mark GM Aarts. “Natural genetic variation in plant photosynthesis”. In: Trends in plant science 16.6 (2011), pp. 327–335. DOI: https://doi.org/10.1016/j.tplants.2011.02.005

Hamza Hussain, Khalid Al Tajir, Rashid Habib, Saiyyad Abboud, and Syed Fadel. “The Effects of Political Polarization on Financial Decision Making”. In: Fusion of Multidisciplinary Research, An International Journal (FMR) 4.1 (2023), pp. 420–431.

David Roy Smith and Patrick J Keeling. “Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes”. In: Proceedings of the National Academy of Sciences 112.33 (2015), pp. 10177–10184. DOI: https://doi.org/10.1073/pnas.1422049112

Marco Pellino, Diego Hojsgaard, Thomas Schmutzer, Uwe Scholz, Elvira Hörandl, Heiko Vogel, and Timothy F Sharbel. “Asexual genome evolution in the apomictic R anunculus aurico-mus complex: examining the effects of hybridization and mutation accumulation”. In: Molecular Ecology 22.23 (2013), pp. 5908–5921. DOI: https://doi.org/10.1111/mec.12533

Brandon S Gaut, Maud Le Thierry d’Ennequin, Andrew S Peek, and Mark C Sawkins. “Maize as a model for the evolution of plant nuclear genomes”. In: Proceedings of the National Academy of Sciences 97.13 (2000), pp. 7008–7015. DOI: https://doi.org/10.1073/pnas.97.13.7008

Downloads

Published

2024-01-24

How to Cite

Manuela Horvat, Valentina Novak, Frederik Antunovic, & Dario Blazevic. (2024). Reflecting on the Mutation Rate Variability in Plant Genomes: An In-depth Analysis. Fusion of Multidisciplinary Research, An International Journal, 5(1), 556-567. https://doi.org/10.63995/TZCK7098