DOI: 10.5061/dryad.4xgxd25g9
title: Transposable element libraries from 101 fish

description: Repetitive DNA make up a considerable fraction of most eukaryotic genomes.
 In fish, transposable element (TE) activity has coincided with rapid
 species diversification. Here, we annotated the repetitive content in 100
 genome assemblies, covering the major branches of the diverse lineage of
 teleost fish. We investigated if TE content correlates with family level
 net diversification rates and found support for a weak negative
 correlation. Further, we found that TE proportion correlate to genome
 size, but not to the proportion of short tandem repeats (STRs), which
 implies independent evolutionary paths. Marine and freshwater fish have
 large differences in STR content. The most extreme propagation was found
 in the genomes of codfish species and Atlantic herring. Such a high
 density of STRs is likely to increase the mutational load, which we
 propose could be counterbalanced by high fecundity as seen in codfishes
 and herring.
description: For TE annotation, we used a
 variant of the computational pipeline that is more thoroughly described in
 (Tørresen et al.
 2017), available at
 https://github.com/uio-cels/Repeats. The pipeline includes multiple TE detection steps
 using different tools, steps for removing non-TEs from the detected
 sequences and steps for classifying the elements. For the initial
 detection step, we used RepeatModeler (v. 1.0.8) (Smit & Hubley
 2008-2015) and LTRharvest (part of GenomeTools v. 1.5.7) (Ellinghaus et
 al. 2008). RepeatModeler detects all sorts of repetitive sequences and
 LTRharvest is specialized for detecting LTR-RTs. Using BLASTX, TEs with
 sequences matching known non-TEs in UniProtKB/Swiss-Prot were removed. To
 classify the TEs, we used RepeatClassifier, which is a part of the
 RepeatModeler software. As the tool did not manage to classify all of the
 remaining sequences, additional similarity searches were performed between
 the sequences and a curated library of TE sequences (RepBase v. 20150807),
 using nucleotide BLAST. Finally, we built Hidden Markov Model profiles
 from the detected sequences using HMMER (v. 3.1b1) (Wheeler & Eddy
 2013) and compared the profiles with HMM profiles from databases
 downloaded from GyDB.org (Llorens et al. 2011) and dfam.org (Hubley et al. 2016), using the
 nhmmer feature included in HMMER. This resulted in additional sequences being
 classified at the class and subclass level. The pipeline resulted in one
 <em>de novo</em> library per assembly, which contained the
 consensus sequences of the interspersed repeats detected in each assembly.
description: This repository contain one <em>de novo</em> library
 (FASTA file) per genome assembly. The results of masking each genome
 assembly with RepeatMasker using these<em> de novo</em>
 libraries can be found at
 https://doi.org/10.6084/m9.figshare.8280800.
description: # Teleost TE libraries *** This repository contain de novo libraries of
 transposable element (TE) consensus sequences (FASTA file), one per genome
 assembly. The results of masking each genome assembly with RepeatMasker
 using these de novo libraries can be found at
 https://doi.org/10.6084/m9.figshare.8280800. ## Description of the data
 and file structure Each file is one TE library (FASTA file) that can be
 used to mask a genome assembly. To generate the libraries, we used a
 variant of the computational pipeline that is more thoroughly described in
 (Trresen et al. 2017), available at https://github.com/uio-cels/Repeats.
 The pipeline includes multiple TE detection steps using different tools,
 steps for removing non-TEs from the detected sequences and steps for
 classifying the elements. For the initial detection step, we used
 RepeatModeler (v. 1.0.8) (Smit & Hubley 2008-2015) and LTRharvest
 (part of GenomeTools v. 1.5.7) (Ellinghaus et al. 2008). RepeatModeler
 detects all sorts of repetitive sequences and LTRharvest is specialized
 for detecting LTR-RTs. Using BLASTX, TEs with sequences matching known
 non-TEs in UniProtKB/Swiss-Prot were removed. To classify the TEs, we used
 RepeatClassifier, which is a part of the RepeatModeler software. As the
 tool did not manage to classify all of the remaining sequences, additional
 similarity searches were performed between the sequences and a curated
 library of TE sequences (RepBase v. 20150807), using nucleotide BLAST.
 Finally, we built Hidden Markov Model profiles from the detected sequences
 using HMMER (v. 3.1b1) (Wheeler & Eddy 2013) and compared the
 profiles with HMM profiles from databases downloaded from GyDB.org
 (Llorens et al. 2011) and dfam.org (Hubley et al. 2016), using the nhmmer
 feature included in HMMER. This resulted in additional sequences being
 classified at the class and subclass level. The pipeline resulted in one
 de novo library per assembly, which contained the consensus sequences of
 the interspersed repeats detected in each assembly. ## Sharing/Access
 information The source genome assemblies used to generate the consensus
 libraries was retrieved from the following sources: SOURCE SPECIES
 Malmstrom et al. 2017 Acanthochaenus luetkenii
 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000751415.1\_Midas\_v5/GCA\_000751415.1\_Midas\_v5\_genomic.fna.gz Amphilophus citrinellus Malmstrom et al. 2017 Anabas testudineus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000695075.1\_Anguilla\_anguilla\_v1\_09\_nov\_10/GCA\_000695075.1\_Anguilla\_anguilla\_v1\_09\_nov\_10\_genomic.fna.gz Anguilla anguilla ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000470695.1\_japanese\_eel\_genome\_v1\_25\_oct\_2011\_japonica\_c401b400k25m200\_sspacepremiumk3a02n24\_extra.final.scaffolds/GCA\_000470695.1\_japanese\_eel\_genome\_v1\_25\_oct\_2011\_japonica\_c401b400k25m200\_sspacepremiumk3a02n24\_extra.final.scaffolds\_genomic.fna.gz Anguilla japonica Musilova et al. 2018 Anoplogaster cornuta Malmstrom et al. 2017 Antennarius striatus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000239415.1\_AstBur1.0/GCF\_000239415.1\_AstBur1.0\_genomic.fna.gz Astatotilapia burtoni ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000372685.1\_Astyanax\_mexicanus-1.0.2/GCF\_000372685.1\_Astyanax\_mexicanus-1.0.2\_genomic.fna.gz Astyanax mexicanus Malmstrom et al. 2017 Bathygadus melanobranchus Malmstrom et al. 2017 Benthosema glaciale Malmstrom et al. 2017 Beryx splendens ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000788275.1\_BP.fa/GCA\_000788275.1\_BP.fa\_genomic.fna.gz Boleophthalmus pectinirostris Malmstrom et al. 2017 Borostomias antarcticus Malmstrom et al. 2017 Brosme brosme Malmstrom et al. 2017 Brotula barbata SRX360276, GenBank, see Musilova et al. 2018 Caranx ignobilis SRX360285, GenBank, see Musilova et al. 2018 Caranx melampygus Malmstrom et al. 2017 Carapus acus Musilova et al. 2018 Cetomimus sp Malmstrom et al. 2017 Chaenocephalus aceratus Malmstrom et al. 2017 Chatrabus melanurus Malmstrom et al. 2017 Chromis chromis SRX203077, GenBank, see Musilova et al. 2018 Clupea harengus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000523025.1\_Cse\_v1.0/GCF\_000523025.1\_Cse\_v1.0\_genomic.fna.gz Cynoglossus semilaevis ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000776015.1\_ASM77601v1/GCA\_000776015.1\_ASM77601v1\_genomic.fna.gz Cyprinodon nevadensis ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000776015.1\_ASM77601v1/GCA\_000776015.1\_ASM77601v1\_genomic.fna.gz Cyprinodon variegatus SRX317090, GenBank, see Musilova et al. 2018 Cyprinus carpio Malmstrom et al. 2017 Cyttopsis rosea ftp://ftp.ensembl.org/pub//release-78/fasta/danio\_rerio/dna/Danio\_rerio.Zv9.dna.toplevel.fa.gz Danio rerio ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000689215.1\_seabass\_V1.0/GCA\_000689215.1\_seabass\_V1.0\_genomic.fna.gz Dicentrarchus labrax Musilova et al. 2018 Diretmoides pauciradiatus Musilova et al. 2018 Diretmus argenteus SRX554947, GenBank, see Musilova et al. 2018 Electrophorus electricus ERX432347, GenBank, see Musilova et al. 2018 Epinephelus aeneus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000721915.2\_ASM72191v2/GCF\_000721915.2\_ASM72191v2\_genomic.fna.gz Esox lucius ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000826765.1\_Fundulus\_heteroclitus-3.0.2/GCF\_000826765.1\_Fundulus\_heteroclitus-3.0.2\_genomic.fna.gz Fundulus heteroclitus Malmstrom et al. 2017 Gadus morhua ftp://ftp.ensembl.org/pub//release-78/fasta/gasterosteus\_aculeatus/dna/Gasterosteus\_aculeatus.BROADS1.dna.toplevel.fa.gz Gasterosteus aculeatus Musilova et al. 2018 Gephyroberyx darwinii Malmstrom et al. 2017 Guentherus altivela Malmstrom et al. 2017 Helostoma temminkii Malmstrom et al. 2017 Holocentrus rufus Musilova et al. 2018 Hoplostethus atlanticus Malmstrom et al. 2017 Lampris guttatus Malmstrom et al. 2017 Lamprogrammus exutus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000742935.1\_ASM74293v1/GCF\_000742935.1\_ASM74293v1\_genomic.fna.gz Larimichthys crocea ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000242695.1\_LepOcu1/GCF\_000242695.1\_LepOcu1\_genomic.fna.gz Lepisosteus oculatus Malmstrom et al. 2017 Lesueurigobius cf. sanzoi Musilova et al. 2018 (unpublished) Lophius vaillanti Malmstrom et al. 2017 Macrourus berglax Malmstrom et al. 2017 Merluccius polli ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000238955.2\_M\_zebra\_UMD1/GCF\_000238955.2\_M\_zebra\_UMD1\_genomic.fna.gz Metriaclima zebra Malmstrom et al. 2017 Monocentris japonica SRX218060, GenBank, see Musilova et al. 2018 Monopterus albus Malmstrom et al. 2017 Mora moro Malmstrom et al. 2017 Myoxocephalus scorpius Malmstrom et al. 2017 Myripristis jacobus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000239395.1\_NeoBri1.0/GCF\_000239395.1\_NeoBri1.0\_genomic.fna.gz Neolamprologus brichardi Malmstrom et al. 2017 Neoniphon sammara ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000735185.1\_NC01/GCF\_000735185.1\_NC01\_genomic.fna.gz Notothenia coriiceps Musilova et al. 2018 Opsanus beta ftp://ftp.ensembl.org/pub//release-78/fasta/oreochromis\_niloticus/dna/Oreochromis\_niloticus.Orenil1.0.dna.toplevel.fa.gz Oreochromis niloticus ftp://ftp.ensembl.org/pub//release-78/fasta/oryzias\_latipes/dna/Oryzias\_latipes.MEDAKA1.dna.toplevel.fa.gz Oryzias latipes Malmstrom et al. 2017 Osmerus eperlanus Malmstrom et al. 2017 Parablennius parvicornis Malmstrom et al. 2017 Parasudis fraserbrunneri Malmstrom et al. 2017 Perca fluviatilis Malmstrom et al. 2017 Percopsis transmontana ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000787095.1\_PS.fa/GCA\_000787095.1\_PS.fa\_genomic.fna.gz Periophthalmodon schlosseri ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000787105.1\_PM.fa/GCA\_000787105.1\_PM.fa\_genomic.fna.gz Periophthalmus magnuspinnatus SRX423854, GenBank, see Musilova et al. 2018 Pimephales promelas ftp://ftp.ensembl.org/pub//release-78/fasta/poecilia\_formosa/dna/Poecilia\_formosa.PoeFor\_5.1.2.dna.toplevel.fa.gz Poecilia formosa ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000633615.1\_Guppy\_female\_1.0\_MT/GCF\_000633615.1\_Guppy\_female\_1.0\_MT\_genomic.fna.gz Poecilia reticulata Malmstrom et al. 2017 Polymixia japonica Malmstrom et al. 2017 Pseudochromis fuscus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000787555.1\_Pyoko\_1.0/GCA\_000787555.1\_Pyoko\_1.0\_genomic.fna.gz Pseudopleuronectes yokohamae ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000239375.1\_PunNye1.0/GCF\_000239375.1\_PunNye1.0\_genomic.fna.gz Pundamilia nyererei Malmstrom et al. 2017 Regalecus glesne Malmstrom et al. 2017 Rondeletia loricata ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000233375.1\_ICSASG\_v2/GCF\_000233375.1\_ICSASG\_v2\_genomic.fna.gz Salmo salar ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000787155.1\_SH.fa/GCA\_000787155.1\_SH.fa\_genomic.fna.gz Scartelaos histophorus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_001005745.2\_aro\_v2/GCA\_001005745.2\_aro\_v2\_genomic.fna.gz Scleropages formosus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000475235.1\_Snig1.0/GCA\_000475235.1\_Snig1.0\_genomic.fna.gz Sebastes nigrocinctus Malmstrom et al. 2017 Sebastes norvegicus Malmstrom et al. 2017 Selene dorsalis Malmstrom et al. 2017 Spondyliosoma cantharus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF\_000690725.1\_Stegastes\_partitus-1.0.2/GCF\_000690725.1\_Stegastes\_partitus-1.0.2\_genomic.fna.gz Stegastes partitus Malmstrom et al. 2017 Stylephorus chordatus Malmstrom et al. 2017 Symphodus melops Musilova et al. 2018 (unpublished) Syngnathus typhle Musilova et al. 2018 (unpublished) Synodus synodus ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000400755.1\_version\_1\_of\_Takifugu\_flavidus\_genome/GCA\_000400755.1\_version\_1\_of\_Takifugu\_flavidus\_genome\_genomic.fna.gz Takifugu flavidus ftp://ftp.ensembl.org/pub//release-78/fasta/takifugu\_rubripes/dna/Takifugu\_rubripes.FUGU4.dna.toplevel.fa.gz Takifugu rubripes ftp://ftp.ensembl.org/pub//release-78/fasta/tetraodon\_nigroviridis/dna/Tetraodon\_nigroviridis.TETRAODON8.dna.toplevel.fa.gz Tetraodon nigroviridis Malmstrom et al. 2017 Thunnus albacares ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA\_000418415.1\_Thunnus\_orientalis\_ver\_Ba\_1.0/GCA\_000418415.1\_Thunnus\_orientalis\_ver\_Ba\_1.0\_genomic.fna.gz Thunnus orientalis Malmstrom et al. 2017 Trisopterus minutus Malmstrom et al. 2017 Typhlichthys subterraneus ftp://ftp.ensembl.org/pub//release-78/fasta/xiphophorus\_maculatus/dna/Xiphophorus\_maculatus.Xipmac4.4.2.dna.toplevel.fa.gz Xiphophorus maculatus Malmstrom et al. 2017 Zeus faber Malmstrom et al. 2017 Arctogadus glacialis Malmstrom et al. 2017 Molva molva Malmstrom et al. 2017 Lota lota Malmstrom et al. 2017 Brosme brosme Malmstrom et al. 2017 Merluccius merluccius Malmstrom et al. 2017 Merluccius polli Malmstrom et al. 2017 Melanonus zugmayeri Malmstrom et al. 2017 Macrourus berglax Malmstrom et al. 2017 Malacocephalus occidentalis Malmstrom et al. 2017 Bathygadus melanobranchus Malmstrom et al. 2017 Boreogadus saida Malmstrom et al. 2017 Muraenolepis marmoratus Malmstrom et al. 2017 Bregmaceros cantori Malmstrom et al. 2017 Mora moro Malmstrom et al. 2017 Trisopterus minutus Malmstrom et al. 2017 Trachyrincus scabrus Malmstrom et al. 2017 Pollachius virens Malmstrom et al. 2017 Melanogrammus aeglefinus Malmstrom et al. 2017 Merlangius merlangus Malmstrom et al. 2017 Theragra chalcogramma Malmstrom et al. 2017 Gadiculus argenteus Malmstrom et al. 2017 Phycis phycis Malmstrom et al. 2017 Phycis blennoides Malmstrom et al. 2017 Gadus morhua