2.4 Repetitive sequence annotation
We annotated the repetitive sequences in the P. leopardus genome with both homology searching in known repeat database and de novopredictions. Known repeats were identified using RepeatMasker (v3.3.0) (Taraio-Graovac & Chen, 2009) with the RepBase TE library (v14.06) (Bao et al., 2015). RepeatProteinMask (v3.2.2) implemented in RepeatMasker was used to detect the TE-relevant proteins. Novel repeats were predicted using RepeatModeler (http://www.repeatmasker.org) based on thede novo repeat library constructed with LTR_Finder (Xu & Wang, 2007) and RepeatScout (Price et al., 2005). In addition, we used Tandem Repeat Finder (TRF, v4.09) (Benson, 1999) to identify the tandem repeats in the genome with parameters of “Match=2, Mismatch=7, Delta=7, PM=80, PI=10, Minscore=50, and MaxPerid=2000”.