Repeats and transposable elements annotation
For repetitive sequence annotation, tandem repeats were annotated using Tandem Repeat Finder (TRF) (http://tandem.bu.edu/trf/trf.html, v4.10) (Benson 1999) with default parameters. For transposable elements (TEs) annotation, both RepeatProteinMask (RM-BLASTX) and RepeatMasker (open-4.0.7) (Bedell et al. 2000) were used. RepeatProteinMask software was used to search TEs in its protein database, and RepeatMasker software was used for de novolibraries and the Repbase library (zebrafish). The de novo repeat libraries were analyzed by RepeatModeler software with default parameters. The insertion time of each TE was calculated usingK /2r (Bowen & McDonald 2001; SanMiguel et al. 1998).K represents the kimura value, which was extracted from the RepeatMasker analysis, and r represents the evolutionary rate acquired from the r8s analysis (Sanderson 2003).