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.