Repetitive elements identification
We analyzed repetitive regions in the new assembly using a combination of a de novo transposable elements identification with RepeatModeler v1.0.11 (Smit, & Hubley; RepeatModeler), and a similarity-based search with RepeatMasker v.4.0.7 (Smit, Hubley, & Green; RepeatMasker). For the analysis we used the repetitive elements database built for the version 1 of the D. silvatica draft genome see Sánchez-Herrero et al. (2019) for more details), generated with RepeatModeler, plus Dfam_Consensus-20171107 and RepBase-20181026 databases. The new assembly was masked for these repetitive sequences using the (-xsmall) option of RepeatMasker to be used in the genome annotation steps.