Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

Sessegolo, Camille; Burlet, Nelly; Haudry, Annabelle

doi:10.1098/rsbl.2016.0407

Cited by 70 publications

(89 citation statements)

References 29 publications

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“…Rather, genome size evolution is reliant upon phylogenetic patterns. These results are supported by recent work on genome size evolution in Drosophila species [39]. Here, Sessegolo et al .…”

Section: Discussionsupporting

confidence: 83%

The mode and tempo of genome size evolution in the subgenus Sophophora

Hjelmen

Johnston

2017

PLoS ONE

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Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s Cmean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s Cmean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships.

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Section: Discussionsupporting

confidence: 83%

The mode and tempo of genome size evolution in the subgenus Sophophora

Hjelmen

Johnston

2017

PLoS ONE

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“…Interestingly, we did not observe a significant correlation between the genome size (Fig. 6) and the proportion of LTR-retrotransposons (Spearman correlation test r = 0.41, p -value = 0.07115) whereas it has been shown that the proportion of repeats is correlated with Drosophila genome size, in link with phylogenetic inertia [39]. It is possible that the lack of correlation comes from the fact that we are considering only LTR-retrotransposons.…”

Section: Resultsmentioning

confidence: 72%

Evolutionary history of LTR-retrotransposons among 20 Drosophila species

Bargues

Lerat

2017

Mobile DNA

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BackgroundThe presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, Drosophila melanogaster and D. simulans. However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus Sophophora and Drosophila, revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content. The identification of some consensus sequences of TEs from the various sequenced Drosophila species allowed to get an idea concerning their variety in term of diversity of superfamilies but the used classification remains very elusive and ambiguous.ResultsWe choose to focus on LTR-retrotransposons because they represent the most widely represented class of TEs in the Drosophila genomes. In this work, we describe for the first time the phylogenetic relationship of each LTR-retrotransposon family described in 20 Drosophila species, compute their proportion in their respective genomes and identify several new cases of horizontal transfers.ConclusionAll these results allow us to have a clearer view on the evolutionary history of LTR retrotransposons among Drosophila that seems to be mainly driven by vertical transmissions although the implications of horizontal transfers, losses and intra-specific diversification are clearly also at play.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-017-0090-3) contains supplementary material, which is available to authorized users.

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“…While species with higher 47 O'Grady 2006; Clark et al 2007). The sequenced species, show striking differences between TE 63families and orders, and make up differing proportions of the genome, between 5 and 40% across 64 the tree (Sessegolo et al 2016). Additionally, the TE content of two species in the D. affinis 65…”

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confidence: 99%

Transposable element dynamics are consistent across theDrosophilaphylogeny, despite drastically differing content

Hill

2019

Preprint

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1The evolutionary dynamics of transposable elements (TEs) vary across the tree of life and even 2 between closely related species with similar ecologies. In Drosophila, most of the focus on TE 3 dynamics has been completed in Drosophila melanogaster and the overall pattern indicates that 4TEs show an excess of low frequency insertions, consistent with their fitness cost in the genome. 5However, work outside of D. melanogaster, in the species Drosophila algonquin, suggests that 6 this situation may not be universal, even within Drosophila. Here we test whether the pattern 7 observed in D. melanogaster is similar across five Drosophila species that share a common 8 ancestor more than fifty million years ago. We find that, for most TE families and orders, the 9 patterns are broadly conserved between species, suggesting TEs are primarily costly, and dynamics 10 are conserved in orthologous regions of the host genome. These results suggest that most TEs 11 retain similar activities and fitness costs across the Drosophila phylogeny suggesting little 12 evidence of drift in the dynamics of TEs across the phylogeny. 13 Lu and Clark 2010). Using small RNAs transcribed from TE sequences, the 31 piRNA system targets and degrades complementary TE mRNAs and cause heterochromatin 32 formation on similar TE insertions (Obbard et al. 2009;Blumenstiel 2011;Lee 2015; Senti et al. 33 2015). Within this suppression system, the extent of silencing is then dependent on the expression 34 and copy number of TEs, resulting in the copy number regulation seen in Drosophila (Lee and 35 14Langley 2010). However, the piRNA system can cause the propagation of heterochromatic 36 silencing marks around TE insertions, resulting in the silencing of nearby genes and position effect 37 variegation (Lee and Langley 2010; Lee 2015). This deleterious side effect, in combination with 38 the deleterious effects of TE insertions suggests TE insertions should be rare in euchromatic 39regions (Charlesworth and Langley 1989;Charlesworth et al. 1997;Lee and Langley 2010). 40Within this model, TEs will enter a genome and spread rapidly through a burst of 41 unsuppressed transposition (Kofler et al. 2012;Lee and Langley 2012). The TE will be silenced 42 via the piRNA system and regulated so long as piRNAs are produced against the TE (Senti and 43 Brennecke 2010;Blumenstiel 2011). Following this, you should expect larger genomes with fewer 44active TEs, such as mammals, to have higher TE abundances and TE insertion frequency spectra 45 (IFS) showing no skew towards rare insertions as TE insertions are on average, less costly (Figure 461) (Lee and Langley 2012; Hellen and Brookfield 2013a; Lee 2015). While species with higher 47 O'Grady 2006; Clark et al. 2007). The sequenced species, show striking differences between TE 63families and orders, and make up differing proportions of the genome, between 5 and 40% across 64 the tree (Sessegolo et al. 2016). Additionally, the TE content of two species in the D. affinis 65

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Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

Cited by 70 publications

References 29 publications

The mode and tempo of genome size evolution in the subgenus Sophophora

The mode and tempo of genome size evolution in the subgenus Sophophora

Evolutionary history of LTR-retrotransposons among 20 Drosophila species

Transposable element dynamics are consistent across theDrosophilaphylogeny, despite drastically differing content

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