A combined strategy based on homology alignment and de novo search was used to identify repeat elements in the G. elata genome. For de novo prediction of transposable elements (TEs), we used RepeatModeler (http://www.repeatmasker.org/RepeatModeler.html), RepeatScout36, and LTR-Finder37 with default parameters. For alignment of homologous sequences to identify repeats in the assembled genome, we used RepeatProteinMask and RepeatMasker (http://www.repeatmasker.org) with the rebase library38. Transposable elements overlapping with the same type of repeats were integrated, while those with low scores were removed if they overlapped more than 80 percent of their lengths and belonged to different types (Supplementary Table 7).