2.5 Annotation of repeats
The repeat sequences of C. japonica were marked by the combining of RepeatModeler v2.0.2 and RepeatMasker v4.1.2 (http://www.repeatmasker.org/). Firstly, a de novo repeat database was built by RepeatModeler. Then using RepeatMasker to perform the repeat sequence annotation based on the Repbase (https://www.girinst.org/server/RepBase/index.php). The random repeats were detected by TRF (Tandem Repeats Finder) v4.09 (Benson, 1999). And the sequence search engine was RMBlast v2.11.0 (http://www.repeatmasker.org/RMBlast.html) for sequence alignment.