Two approaches were used to discover repeat elements: de novo predictions and homolog-based identifications. RepeatModeler (http://www.repeatmasker.org/RepeatModeler/,vision 1.0.5) and LTR_FINDER39 were used to build a de novo repeat library, followed by analysis with RepeatMasker (http://www.repeatmasker.org, version 3.3.0) to discover TEs. RepeatMasker and RepeatProteinMask were involved in homology-based identifications to detect TEs by comparing them to Repbase.

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