Figure 5. Repeat content varies greatly between drosophilid groups.

For each species, the proportion of each genome annotated with a particular repeat type is depicted. Species relationships were inferred by randomly selecting 250 of the set of BUSCOs (Seppey et al., 2019) that were complete and single-copy in all assemblies. RAxML-NG (Kozlov et al., 2019) was used to build gene trees for each BUSCO then ASTRAL-MP (Yin et al., 2019) to infer a species tree. Repeat annotation was performed with RepeatMasker (Smit et al., 2013) using the Dfam 3.1 (Hubley et al., 2016) and RepBase RepeatMasker edition (Bao et al., 2015) databases. ASTRAL local posterior probabilities are reported at each node.

Figure 5—figure supplement 1. Assembly contiguity is not determined by repeat content.

There is no relationship (Spearman’s ρ=0.036, p=0.725) between repeat content (as annotated by RepeatMasker) in a genome and the contiguity of the resulting assembly.

Figure 5—figure supplement 2. The non-repetitive and repetitive portions of the genome both contribute to genome size differences between drosophilids.

Phylogenetically independent contrasts (PICs) are shown for the number of bases in each genome not annotated as repetitive sequence (x-axis) and the number annotated as repeat by RepeatMasker (y-axis). The red dotted line is the best-fitting line through the origin. A positive relationship between the non-repetitive and repetitive portions of the genome is observed (Spearman’s ρ=0.679, p<2.2e-16), suggesting that both play a role in determining the genome size of drosophilids.