Repeats Annotation
Repeat elements in the M. pygmaea genome were identified with the help of the RepeatMasker v4.0 (Tarailo-Graovac & Chen, 2009) and RepeatModeler v4.07 (Smit & Hubley, 2011) with default settings. Intact long terminal repeat (LTR) retrotransposons were identified with LTRharvest v1.5.10 (Ellinghaus et al., 2008) and LTR_Finder v1.06 (Xu & Wang, 2007) with LTR length set to range from 100-5,000 nt and the length between two LTRs set to 1,000-2,0000 nt. Results were combined using LTR_retriever v1.9 (Ou & Jiang, 2018) and the insertion time (T) was calculated for each LTR retrotransposon (T = K/2r, K: genetic distance) with a substitution rate (r) of 7 × 10−9 substitutions per site per year (Ossowski et al., 2010).