Repeat Elements

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For identifying and masking repeat elements in the coconut genome the pipeline used had following tools,

1. RepeatModeler version 2.0.4 for de novo transposable element (TE) family identification and modeling.
2. LTR retriever version 2.9.0, LTR harvest version 0.6.5 for LTR identification.
3. RECON version 1.08 for identified repeat element classification.
4. RepeatMasker version 4.1.5 for masking the annotated repeat elements.

Repeatmodeler identified and classified repeat elements found in the coconut genome with the help of RepBase Library(Release 20181026). Repeatmasker was used to mask the coconut genome assembly with the identified repeat library. Total repeats identified in the coconut genome constitute 81.64% of the genome that is approximately 2.19Gb of 2.68 Gb coconut genome assembly. LTR elements are the most abundant repeat element class making 53.76 % of the genome assembly. LTR copia and LTR gypsy elements the most abundant LTR elements in the genome occupying 40.57% and 12.98% of the genome.