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

Abstract

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

Transposable elements in Drosophila

“…the relative abundance of the different TE orders is globally conserved across studies and similar to what is represented in Fig. 2 [55,102,103,105]. Retrotransposons, and essentially LTRs and LINEs (respectively 12% and 5% of the genome in our analysis), contribute substantially to D. melanogaster TE content.…”

“…Retrotransposons can be divided into five orders: long terminal repeat (LTR) retrotransposons, Dictyostelium intermediate repeat sequence (DIRS)-like elements, Penelope-like elements (PLEs), long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). All of them are present in Drosophila, but LTR retrotransposons and LINEs are by far the most abundant [20,55].…”

“…We used a combination of RepeatMasker, to identify genomic fragments homologous to a library of Drosophila TE consensus sequences available in the RepBase database, and the bioinformatic tool OneCodeToFindThemAll to reconstitute TE copies [56, 100,101]. As previously reported, D. melanogaster genome contains~20% of TEs [55,102]. Note that a significant variation exists regarding these estimates [103][104][105].…”

“…At the intraspecific level, genome size, which is correlated to TE abundance in Drosophila, is variable within populations of both D. simulans and D. melanogaster. This suggests that TE contents may change between populations, at least quantitatively [20,55,115]. In addition, the discovery of hybrid dysgenesis, i.e.…”

Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways

“…Before we compare the endogenous piRNA clusters between Drosophilids and Culicids, we first review how genomic transposon content varies between Drosophilid, anopheline, and culicine lineages ( Figure 1 E). With its well-curated compact genome and ~140 manually annotated transposon families [ 61 , 62 ], Drosophila is the quintessential basis for dipteran comparisons. Despite some variations in estimates of transposon content across Drosophilid genomes [ 62 , 63 , 64 ], the relative abundance of transposons is conserved [ 62 , 65 ] and piRNA abundance correlates well with transposon load [ 66 , 67 ].…”