2.8 Repetitive element annotation
Simple sequence repeats (SSRs) of the C. undulatus genome were first identified using GMATo (Wanget al. 2013). After SSRs were soft-masked, tandem repetitive elements (TREs) were annotated using Tandem Repeat Finder (Benson 1999) with default parameters. When TREs were soft-masked in the genome assembly, the miniature transposable elements (MITE) were identified using MITE-hunter (Han & Wessler 2010) to produce a de novo MITE library, and the long terminal repeat retrotransposons (LTR) were identified using LTR_Finder (Flicek et al. 2014) to obtain ade novo LTR library. Thereafter, MITE and LTR libraries were merged into a de novo transposon library (TE-lib). The genome assembly was hard-masked by TE-lib and annotated to generate a de novo RepMod Library (RepM-lib) using RepeatModeler (http://www.repeatmasker. org). Finally, RepeatMasker (http://www.repeatmasker.org) was used to screen for repeats with homology-based annotation in the TE-lib, RepM-lib, and RepBase databases (Bao et al. 2015).