DOI: 10.5061/dryad.m0cfxpp3h
title: Data from: Transposable element annotation in non-model species - on the benefits of species specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines

description: Transposable elements (TEs) are significant genomic components which can
 be detected either through sequence homology against existing databases or
 de novo, with the latter potentially reducing underestimates of TE
 abundance. Here, we describe the semi-automated generation of a de-novo TE
 library which combines the newly described EDTA pipeline and DeepTE
 classifier in a non-model teleost (Corydoras sp. C115). We assess
 performance using both genomic and transcriptomic input by five metrics:
 (i) abundance (ii) composition (iii) fragmentation (iv) age distributions
 and (v) capture of potential horizontally transferred TEs. We identified
 notable differences in these metrics between different TE libraries, and
 highlight how  library choice can have a major impact on
 TE content estimates in non-model species. This repository incorporates
 six raw (unparsed) Repeat Masker (RM) output files for two genomes
 (Corydoras sp. c115 and Corydoras maculifer) one transcriptome (C.
 maculifer), two Repeat Libraries (one based on the RepBase Danio rerio
 library and one de novo library build on the C. sp. c115 genome). The RM
 ouput files correspond to one homology based transposon search using the
 D. rerio library and one species specific search using the de novo
 library. It also includes a script to acompany horizontal transfer
 analysis and a transposable element renamins script.
description: A ‘de-novo’ TE library was generated for the C. sp. C115 genome
 using the Extensive de-novo TE Annotator (EDTA) (Ou et al., 2019) set to
 the ‘others’ species parameter. We utilised the inbuilt RepeatModeller
 (Smit & Hubley, 2008) support which identifies any remaining TEs
 which might have been overlooked by the EDTA algorithm (--sensitive 1).
 Classifications within this library were refined using DeepTE using the
 predefined metazoan model parameter setting (-m) (Yan et al., 2020).
 TE  identification was performed using RepeatMasker (RM; version 1.332)
 utilising the NCBI/RMBLAST (version 2.6.0+) search engine. This analysis
 was conducted either against the D. rerio Repbase (2018-10-26) entry,
 which was also run through DeepTE (to allow for uniformity in TE
 classification), or the Corydoras-specific library. RM was run under the
 most sensitive (-s) parameter setting in all instances. The genomic and
 transcriptomic RM output files were subsequently parsed through a custom R
 script which (i) removed non-distinct elements by retaining repeats which
 had a higher scoring match whose domain partly include the domain of
 another match, (ii) removed repetitive elements not classed as TEs (e.g.
 microsatellites, simple repeats & sRNAs), (iii) merged elements
 found on the same contig if they had the same name, orientation, and their
 combined sequence length was less than or equal to the corresponding
 reference sequence in RepBase and (iv) removed merged repeats with a
 length less than 80 base pairs. Additionally, for transcriptomic data, if
 multiple identical repeats were found across different transcript
 isoforms, only one was retained. This was to ensure that each repeat
 represented a unique genomic locus. This script is publicly available from
 https://github.com/clbutler/RM_TRIPS."  Additional
 scripts describe a horozontal transfer of transposible elements analysis
 included in the acompanying manuscript. 
description: Please note that the Repeat Masker output files are raw and
 unparsed. To parse data as in the manuscript please use the parse script
 published here: <b id="docs-internal-guid-e6e6b9e3-7fff-62fa-3920-40a9e57abac6">https://github.com/clbutler/RM_TRIPS</b> File List: DanioLib_DeepTE_clean.fasta -&gt; The RepBase Danio library which has been run through the DeepTE program for TE classification Lin1C115wtgdb_EDTADeepTE_cleanLib_V1.1.fasta -&gt; The de novo transposible element library we produced for the Corydoras sp. C115 genome using EDTA and then DeepTE Horizontal_transfer_Analysis_script.R -&gt; The R script used for the horizontal transfer of transposible elements analysis  Unparsed_DanioDeepTElib_CmaculiferGenome_AssemblyNameCM_19_scafSeq.fas.out -&gt; Unparsed Repeat Masker output using DanioLib_DeepTE_clean.fasta as the repeat library and the Corydoras maculifer genome (available on genbank) Unparsed_DanioDeepTElib_CmaculiferSample56_transcriptome.out -&gt; Unparsed Repeat Masker output using DanioLib_DeepTE_clean.fasta as the repeat library and the Corydoras maculifer transcriptome (available on genbank) Unparsed_DanioDeepTElib_CorydorasC115genome_AssemblyNameLin1PacBio.ctg.fa.r3p3_pilon_3.fasta.out -&gt;  Unparsed Repeat Masker output using DanioLib_DeepTE_clean.fasta as the repeat library and the Corydoras sp. C115 genome (available on genbank) Unparsed_DeNovolib_CmaculiferGenome_AssemblyNameCM_19_scafSeq.fas.out -&gt; Unparsed Repeat Masker output using Lin1C115wtgdb_EDTADeepTE_cleanLib_V1.1.fasta as the repeat library and the Corydoras maculifer genome (available on genbank) Unparsed_DeNovolib_CmaculiferSample56_transcriptome.out -&gt; Unparsed Repeat Masker output using Lin1C115wtgdb_EDTADeepTE_cleanLib_V1.1.fasta as the repeat library and the Corydoras maculifer transcriptome (available on genbank) Unparsed_DeNovolib_CorydorasC115genome_AssemblyNameLin1PacBio.ctg.fa.r3p3_pilon_3.fasta.out -&gt; Unparsed Repeat Masker output using Lin1C115wtgdb_EDTADeepTE_cleanLib_V1.1.fasta as the repeat library and the Corydoras sp. C115 genome (available on genbank) Unparsed_DanioDeepTElib_DanioGenome_AccessionNoGCF_000002035.6_GRCz11.out -&gt; Unparsed Repeat Masker output using DanioLib_DeepTE_clean.fasta as the repeat library against the Danio rerio genome (Accession number: GCF_000002035.6_GRCz11)