Comprehensive characterization of repetitive elements in Ilex species (Aquifoliaceae) genomes via RepeatModeler and EDTA pipelines

Description

This dataset comprises sequence libraries (FASTA format) of Long Terminal Repeat Retrotransposons (LTR-RTs) and Helitrons, along with their corresponding intact element annotation files (GFF format), all generated by the EDTA pipeline (Extensive de-novo TE Annotator). Additionally, libraries of general repetitive elements (FASTA format) generated by RepeatModeler are included. The Ilex species analyzed are: I. aquifolium, I. asprella, I. latifolia, I. polyneura, and I. paraguariensis. The resulting repetitive libraries and annotated repetitive loci files are valuable resources and are now available to the interested community for downstream analysis.

Steps to reproduce

Analyzed genomes are available at: https://www.ncbi.nlm.nih.gov/ https://ngdc.cncb.ac.cn/ Methods: EDTA: https://doi.org/10.1186/s13059-019-1905-y RepeatModeler 2.0.1 (Search Engine = rmblast 2.2.27; Dependencies: TRF 4.09, RECON, RepeatScout 1.0.5, RepeatMasker 4.1.0).

Institutions

• CONICET Nordeste

  Corrientes, Corrientes
• Universidad Nacional de Misiones

  Misiones, Posadas
• Instituto de Biologia Subtropical

  Misiones Province, Posadas

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