Quast v4.0 was used to check genome assembly quality with ONT reads, for assembly assessment report see Supplementary Note 2. Repeats and transposable elements were annotated using the RepeatModeler 2.0 and RepeatMasker 4.0.8 pipeline53 with the searching programme of NCBI RMblast v2.9.0. The species-specific repeat library was annotated with RepeatModeler. Afterwards, RepeatMasker was run twice, one using the species-specific repeat library and another one using the repeats in Repbase ( ). All the results were summarized and classified with the perl script buildSummary.pl in the RepeatMasker package, for summary table see Supplementary Note 2.
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