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Genome Size in the UK Fabaceae Flora and How This Relates to Their Nitrogen and Water Tolerance

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Genome Size in the UK Fabaceae Flora and How This Relates to Their Nitrogen and Water Tolerance Genome size in the UK Fabaceae flora and how this relates to their nitrogen and water tolerance Lauren Pollitt 2019 Dissertation submitted for the degree of Master of Science in Plant and Fungal Taxonomy, Diversity and Conservation awarded by Queen Mary, University of London. https://doi.org/10.34885/79 © The Author. All rights reserved. 6 i. Abstract Genome size (GS) is defined as the total DNA amount in the unreplicated nucleus of an organism, often used synonymously with ‘1C value’. GS varies greatly in flowering plants. Nitrogen (N) and water are considered major limiting factors for plant growth, and their availability could correlate with plants’ GS. Nitrogen is one of the main building blocks of DNA; plants with larger genomes may have elevated N requirements. Water is lost through pores in the epidermal leaf surface area called stomata, formed by two guard cells. GS has been shown to positively correlate with guard cell size. Previous studies have demonstrated that smaller guard cells result in reduced water-loss. This study considers whether large genome Fabaceae species are more likely to be excluded from dry, N-limited environments, and whether there is an interaction between N and water availability which affects GS. Ellenberg values were used as a proxy for water and N in habitats. GS of UK Fabaceae flora were obtained from the Royal Botanic Gardens, Kew 2C-value database and flow cytometry measurements. Guard cell measurements were obtained from stomatal peels. Statistical analysis in R revealed statistically significant correlations between genome size, water, nitrogen and their interaction, with one interesting outlier species. Phylogenetic trees, ancestral reconstruction and a phylogenetic least squares model revealed a strong phylogenetic signal in the data. This study demonstrates that N and water availability often has an effect on GS in UK Fabaceae. Subsequent studies should include mycorrhizal association and rhizobia information in relation to sourcing nitrogen and water, and how this affects GS. Key words: DNA - Ellenberg – environment – Fabaceae – flow cytometry - guard cells – phylogenetic tree – stomata 7 ii. Contents i. Abstract……………………………………………………………………………………………………………………….…….6 1. Acknowledgements…………………………………………………………………………………………….……8 2. Introduction………………………………………………………………………………………………………….….9 2.1 Genome size in plants………………………………………………………………………………………………….….9 2.2 UK Fabaceae…………………………………………………………………………………………………………………...9 2.3 The effect of moisture availability on genomes size in plants………………………………………….9-10 2.4 The effect of nitrogen availability on genome size in Fabaceae……………………………………….10-11 2.5 Ellenberg values………………………………………………………………………………………………………………11 2.6 Aims of study…………………………………………………………………………………………………………………..11 3. Materials and Methods……………………………………………………………………………………..….12 3.1 Ellenberg values and database………………………………………………………………………………………..12 3.2 Flow cytometry………………………………………………………………………………………………………………12-13 3.3 Stomatal measurements………………………………………………………………………………………………….13 3.4 Statistical analysis in R………………………………………………………………………………………………….…13 3.5 Phylogenetic reconstruction in R………………………………………………………………………………….…13 4. Results……………………………………………………………………………………………………………….…14 - 15 4.1 The effect of moisture on GS in UK Fabaceae flora; indicated by EF and GCS…………………..14 4.2 The effect of nitrogen, measured by EN, on GS in UK Fabaceae flora……………………………….14 4.3 Interaction between EN and EF on GS…………………................................................................15 4.4 Accounting for phylogenetic nonindependence…………………………………………………………………15 4.5 Phylogenetic ancestral reconstruction………………………………………………………………………………..15 5. Discussion………………………………………………………………………………………………………………16 - 18 5.1 Overall genome size trends in UK Fabaceae……..……..…………………………………………………….….16 5.2 The effects of Nitrogen on GS………………………………………………………………………………………….…16 5.3 The effects of moisture on GS………………………………………………………………………………………….…16 5.4 Outlier Lathyrus sylvestris…………….………………………………………………………………………………….…17 5.5 Evaluation of the study…………………………..………………………………………………………………………...17 5.6 Conclusions…………………………………………………………………………………………………………………….….18 6. Tables and Figures………………………………………………………………………………………………………………19 - 29 6.1 Tables…………………………………………………………………………………………………………………………….…19 – 20 6.2 Figures……………………………………………………………………………………………………………………………..21- 29 7. References…………………………………………………………………………………………………………….30 - 33 8. Appendices and supplementary material………………………………………………………… …..34 - 55 8 1. Acknowledgements I would like to thank my supervisor Professor Andrew Leitch for his time, support and dedication throughout my research project. I thank Dr Ilia Leitch for her guiding wisdom, Dr Robyn Powell for her flow cytometry measurements and expertise and Marie Henniges for her reliable help and insightful contribution throughout. 9 2. Introduction 2.1 Genome size in plants The first genome to be measured in 1951 by Ogur et al. was Lilium longiflorum cv. Croft (Bennet and Leitch, 2005; Greilhuber, 2013). Since then over 8,500 species of plants have been measured, including 3,500 angiosperms, which comprises 1% of angiosperm species, and 485 of angiosperm families (Soltis et al, 2003; Leitch et al., 1998; Pellicer & Leitch, 2014). A staggering 2,400-fold variation in genome size exists in angiosperms (Dodsworth et al., 2015; Guignard et al., 2017; Pellicer et al, 2010; Soltis et al, 2003). Whole-genome-duplication, also called polyploidisation, can cause an increase in genome size (Wendel, 2015). All angiosperms are considered to be paleo-polyploids, having undergone at least one round of polyploidisation in their evolutionary history (Wendel, 2015; Dodsworth, 2016; Guignard et al, 2016). An extreme example is the historically 288-ploid Brassica genus (Wendel, 2015). GS can increase by repeated-sequence DNA or transposable-element proliferation (Dodsworth et al, 2015; Hawkins et al, 2008). A decrease in genome size can be caused by diploidization, a process involving genome-downsizing, which can occur over millennia (Wendel, 2015). Additionally, intrastrand homologous recombination, illegitimate recombination and non- homologous end joining can also drive genome size down (Dodsworth et al., 2015; Hawkins et al, 2008). Genome size and ploidy level are not necessarily linked due to the downsizing process (Soltis, 2003; Pellicer and Leitch, 2014). Considering that the ancestral angiosperm genome was estimated to be <1.4 pg, and the majority of extant angiosperms have small genomes of around 0.2 – 3.5 pg, there appears to be a large-scale genome downsizing trend across angiosperms (Bennett & Leitch, 2005; Dodsworth et al., 2015; Pellicer et al., 2014). GS has been shown to be predictive for seed mass, pollen size, GC content of DNA, flower and shoot phenology, UV radiation sensitivity, time to complete cell cycles and cell size (Bennet, Beaulieu et al., 2008; Vesely et al., 2011; ) This study refers to the ‘1C-value’: DNA amount in one chromosomal set (monoploid) chromosome number n, of the non-replicated gamete nucleus (Greilhuber et al., 2005). This is irrespective of ploidy level and measured in picograms or megabase pairs (Pellicer and Leitch, 2014; Greilhuber et al., 2005; Bennet and Leitch, 2005). The 2C-value is the amount of DNA in a replicated zygotic, diplophasic cell, chromosome number 2n (Greilhuber et al., 2005). 2.2 UK Fabaceae Fabaceae has the third-highest number of species of angiosperm families (LPWG, 2017). Legumes, beans and pulses are economically important crops (LPWG, 2017). The total world exports of pulses have more than doubled from 1990 to 2012, when the value of pulse exports was reported at 9.5 USD. The human diet has included Fabaceae species since the beginning of agriculture, 10,000 years ago (FAO, 2019). The United Nations marked 2016 as the ‘The International Year of Pulses’ which raised awareness about the contribution of Fabaceae crop species in food security (FAO, 2019). This is especially important as the human population continues to grow exponentially and climate change continues to threaten crop production (IPPC, 2014). The UK is a great environment for studying Fabaceae as there are good records of the plant species and the limited number of diverse Fabaceae species make for an excellent case study. 2.3 The effect of moisture availability on genome size in plants Stomata are microscopic pores on the plant leaf surface epidermis, which regulate water vapour loss (transpiration), and CO2 uptake for photosynthesis (Franks and Beerling, 2009). It is widely 10 considered that stomata’s origin 400 mya allowed plants to emerge from the water and colonise land (Franks and Beerling, 2009). Stomata comprise two guard cells which respond to environmental stimuli by opening or closing an aperture, thus adjusting the flow of CO2 and water (Franks and Beerling, 2009). The turgor pressure in guard cells decreases when water is lower, meaning the aperture size reduces (Bertolino et al., 2019). Water use efficiency is higher when stomata are smaller as the stimulus- response time is shorter, meaning guard cells move faster (Bertolino, 2019). In scarce water conditions the stomata react quickly thus conserving as much water as possible (Bertolino, 2019). Maximal stomatal conductance (gmax) is determined by stomatal size and density (Bertolino, 2019). Genome size and guard cell size strongly correlate, and genome size and stomatal density are inversely correlated (Beaulieu et al., 2008; Bertolino et al., 2019; Franks and Beerling,
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