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).