From genome size to trait evolution during angiosperm radiation

Bhadra, Sreetama; Leitch, Ilia J.; Onstein, Renske E.

doi:10.1016/j.tig.2023.07.006

Cited by 14 publications

(15 citation statements)

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“…This relationship indicates that large-genomed species are restricted to occupying smaller ranges, which is likely due to the nucleotypic effects of their genomes hindering their dispersal distance and limiting their ecological niche (Knight & Ackerly, 2002; Beaulieu et al ., 2007, 2008; Veselý et al, 2012; Carta et al, 2022; Bhadra et al ., 2023). This places large-genomed species at a disadvantage compared to their smaller-genomed counterparts that have greater nucleotypic plasticity (Mayerson et al, 2020; Bhadra et al ., 2023) and may thus occupy both large and small ranges (Fig. 2a).…”

Section: Discussionmentioning

confidence: 99%

“…The ’large-genome-constraint’ hypothesis (LGCH) suggests that species with large genomes might face selection pressure against them due to their negative impact on plant anatomy and physiology (Vinogradov, 2003; Knight et al ., 2005). This is because more genomic material occupies a larger volume, influencing the minimum cell size (Cavalier-Smith, 2005; Šímová & Herben, 2012; Bhadra et al ., 2023). Consequently, plants with larger genomes tend to have larger seeds (Knight & Ackerly, 2002; Beaulieu et al ., 2007; Carta et al ., 2022; Bhadra et al ., 2023), a trait linked to smaller distributional ranges (Sonkoly et al ., 2022).…”

Section: Introductionmentioning

confidence: 99%

“…This is because more genomic material occupies a larger volume, influencing the minimum cell size (Cavalier-Smith, 2005; Šímová & Herben, 2012; Bhadra et al ., 2023). Consequently, plants with larger genomes tend to have larger seeds (Knight & Ackerly, 2002; Beaulieu et al ., 2007; Carta et al ., 2022; Bhadra et al ., 2023), a trait linked to smaller distributional ranges (Sonkoly et al ., 2022). Additionally, they possess larger stomatal guard cells (Beaulieu et al, 2008; Veselý et al ., 2012; Bhadra et al ., 2023), which close and open more slowly (Drake et al, 2013; Kardiman & Ræbild, 2018; Lawson & Matthews, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Consequently, plants with larger genomes tend to have larger seeds (Knight & Ackerly, 2002; Beaulieu et al ., 2007; Carta et al ., 2022; Bhadra et al ., 2023), a trait linked to smaller distributional ranges (Sonkoly et al ., 2022). Additionally, they possess larger stomatal guard cells (Beaulieu et al, 2008; Veselý et al ., 2012; Bhadra et al ., 2023), which close and open more slowly (Drake et al, 2013; Kardiman & Ræbild, 2018; Lawson & Matthews, 2020). This might be disadvantageous in, for example, arid environments that demand efficient water management (Veselý et al ., 2020; Bureš et al ., 2023; Šmarda et al ., 2023).…”

Section: Introductionmentioning

confidence: 99%

“…Large genomes may thus limit species’ dispersal abilities and have narrower ecological niches, potentially resulting in smaller geographic ranges (Sheth et al ., 2020). In contrast, smaller genomes offer more flexibility in cell size (Beaulieu et al ., 2007; Beaulieu et al ., 2008; Veselý et al ., 2012; Meyerson et al ., 2020; Bhadra et al ., 2023), have faster rates of cell division (Francis et al ., 2008; Šímová & Herben, 2012), and lower P and N demands (Šmarda et al ., 2013; Peng et al ., 2022) allowing greater plasticity in range size.…”

Section: Introductionmentioning

confidence: 99%

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The global distribution of angiosperm genome size is shaped by climate

Bureš

Elliott

Veselý

et al. 2022

Preprint

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(1) Evolution of genome size is shaped by various intrinsic and extrinsic factors. We explored three long-standing hypotheses concerning factors shaping the global distribution of genome size: the mutational hazard hypothesis, the polyploidy-mediated hypothesis and the climate-mediated hypothesis. (2) We compiled the largest genome size dataset to date, encompassing >5% of known angiosperm species and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms across all continents. (3) Angiosperm species with large range sizes only have small genomes, consistent with the mutational hazard hypothesis. We also uncovered a unique latitudinal pattern in the distribution of genome size diversity. Climate had a strong effect on the latitudinal pattern in genome size, while the effect of polyploidy was small. Contrary to the unimodal latitudinal patterns found for plant size traits and polyploidy, the increase in angiosperm genome sizes from the equator to 40-50 degrees N/S is probably mediated by different (mostly climatic) mechanisms from those underpinning the decrease in genome sizes observed from 40-50 degrees northwards. (4) Overall, our global analyses highlight that species range size and climate factors are the main drivers shaping the global distribution of angiosperm genome sizes, with their relative importance varying across the latitudinal gradient.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The global distribution of angiosperm genome size is shaped by climate

Bureš

Elliott

Veselý

et al. 2022

Preprint

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Species‐tree topology impacts the inference of ancient whole‐genome duplications across the angiosperm phylogeny

McKibben,

Finch,

Barker

2024

American J of Botany

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PremiseThe history of angiosperms is marked by repeated rounds of ancient whole‐genome duplications (WGDs). Here we used state‐of‐the‐art methods to provide an up‐to‐date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species‐tree hypotheses.MethodsWe used the distribution synonymous divergences (Ks) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss.ResultsThe predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. Ks‐based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species‐tree inference can still produce spurious WGD hypotheses, regardless of method used.ConclusionsHere we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

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The smallest angiosperm genomes may be the price for effective traps of bladderworts

Zedek,

Šmerda,

Halasová

et al. 2024

Annals of Botany

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Background Species of the carnivorous family Lentibulariaceae exhibit the smallest genomes in flowering plants. We explored the hypothesis that their minute genomes result from the unique mitochondrial cytochrome c oxidase (COX) mutation. The mutation may boost mitochondrial efficiency, which is especially useful for suction-bladder traps of Utricularia, but also increase DNA-damaging reactive oxygen species, leading to genome shrinkage through deletion-biased DNA repair. We aimed to explore this mutation's impact on genome size, providing insights into genetic mutation roles in plant genome evolution under environmental pressures. Methods We compiled and measured genome and mean chromosome sizes for 127 and 67 species, respectively, representing all three genera (Genlisea, Pinguicula, and Utricularia) of Lentibulariaceae. We also isolated and analyzed COX sequences to detect the mutation. Through phylogenetic regressions and Ornstein-Uhlenbeck models of trait evolution, we assessed the impact of the COX mutation on the genome and chromosome sizes across the family. Results Our findings reveal significant correlations between the COX mutations and smaller genome and chromosome sizes. Specifically, species carrying the ancestral COX sequence exhibited larger genomes and chromosomes than those with the mutation. This evidence supports the notion that the COX mutation contributes to genome downsizing, with statistical analyses confirming a directional evolution towards smaller genomes in species harboring these mutations. Conclusions Our study confirms that the COX mutation in Lentibulariaceae is associated with genome downsizing, likely driven by increased reactive oxygen species production and subsequent DNA damage requiring deletion-biased repair mechanisms. While boosting mitochondrial energy output, this genetic mutation compromises genome integrity and may potentially affect recombination rates, illustrating a complex trade-off between evolutionary advantages and disadvantages. Our results highlight the intricate processes by which genetic mutations and environmental pressures shape genome size evolution in carnivorous plants.

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From genome size to trait evolution during angiosperm radiation

Cited by 14 publications

References 60 publications

The global distribution of angiosperm genome size is shaped by climate

The global distribution of angiosperm genome size is shaped by climate

Species‐tree topology impacts the inference of ancient whole‐genome duplications across the angiosperm phylogeny

The smallest angiosperm genomes may be the price for effective traps of bladderworts

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