DOI: 10.5061/dryad.7pvmcvdxv
title: A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus

description: Despite increasing sequencing efforts, numerous fish families still lack a
 reference genome, which complicates genetic research. One such
 understudied family is the sand lances (Ammodytidae, literally: ‘sand
 burrower’), a globally distributed clade of over 30 fish species that tend
 to avoid tidal currents by burrowing into the sand. Here, we present the
 first annotated chromosome-level genome assembly of the great sand eel
 (Hyperoplus lanceolatus). The genome assembly was generated using Oxford
 Nanopore Technologies long sequencing reads and Illumina short reads for
 polishing. The final assembly has a total length of 808.5 Mbp, of which
 97.1% were anchored into 24 chromosome-scale scaffolds using
 proximity-ligation scaffolding. The assembly is highly contiguous with a
 scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a
 BUSCO completeness score of 96.9%. The presented genome assembly is a
 valuable resource for future studies of sand lances, as they are of great
 ecological and commercial importance and may also contribute to studies
 aiming to resolve the suprafamiliar taxonomy of bony fishes.
description: <strong>Genome assembly <br></strong>
 We assembled the genome of <em>Hyperoplus</em>
 <em>lanceolatus</em> from Oxford Nanopore (ONT) reads using
 WTDBG2 v. 2.5 (Ruan & Li, 2019) using the preset for ONT reads
 (flag '-x ont') followed by three iterations of long-read
 polishing with racon v.1.4.3 (Vaser et al., 2017), one iteration of
 polishing with Medaka v.0.11.5 (Oxford Nanopore Technologies LTD., 2018)
 and three iterations of short-read polishing with pilon v.1.23 (Walker et
 al., 2014). The assembly was scaffolded into chromosome-scale scaffolds
 with the Dovetail Genomics´ HiRise pipeline (Putnam et al., 2016) using
 proximity-ligation data generated by the Dovetail Omni-C kit.
 Subsequently, gap-closing was performed using TGS-GapCloser v.1.1.1 (Xu et
 al., 2020), followed by the removal of haplotigs with purge_dups v.1.2.5
 (Guan et al., 2020). The resulting final assembly, incl. the mitochondrial
 genome generated with MitoZ v.2.4 (Meng et al., 2019), can be found under
 the filename:  
 TBG_H_lanceolatus_asm_v1.1.fasta 
 <strong>Transcriptome</strong> A
 transcriptome was assembled using the best practice guidelines described
 at https://informatics.fas.harvard.edu/best-practices-for-de-novo-transcriptome-assembly-with-trinity.html from Illumina RNAseq data generated from brain, heart, gill, muscle, liver, gonad, and pyloric gland tissue.  The transcriptome can be found under the file name: Hlan002_transcriptome_cleaned_for_ncbi_final.fasta <strong>Annotation</strong> Prior to gene annotation, we used RepeatModeler v. 2.0.1 (Flynn et al., 2020) for the generation of a de novo repeat library. This library was combined with an Actinopterygii-specific library from RepBase (Bao et al., 2015) and used as a custom repeat library for the masking of repeats with RepeatMasker v.4.1.0 (http://www.repeatmasker.org/RMDownload.html). First, we hard-masked all repeats in the assembly and in addition, we generated a masked assembly with hard-masked interspersed repeats andsoft-masked simple repeats. Both the masked assembly files, the de novo repeat library, and the related RepeatMasker output files can be found under the filenames: De Novo Repeat Library:  consensi.fa.classified all repeats hard-masked: TBG_H_lanceolatus_asm_final.purged_mtgenome.fa.masked TBG_H_lanceolatus_asm_final.purged_mtgenome.fa.tbl TBG_H_lanceolatus_asm_final.purged_mtgenome.fa.out Interspersed repeats hardmasked: TBG_H_lanceolatus_asm_final_hardmaskedTEs.fasta TBG_H_lanceolatus_asm_final_hardmaskedTEs.out TBG_H_lanceolatus_asm_final_hardmaskedTEs.tbl Interspersed repeats hardmasked (see above) and simple repeats soft-masked: TBG_H_lanceolatus_asm_final_hardmaskedTEs_softmaskedSR.fasta TBG_H_lanceolatus_asm_final_hardmaskedTEs_softmaskedSR.out TBG_H_lanceolatus_asm_final_hardmaskedTEs_softmaskedSR.tbl Homology-based gene prediction was performed with the GeMoMa pipeline v.1.7.1 with mapped RNAseq data as evidence and the following five references: <em>Acanthochromis</em> <em>polyacanthus</em> (GCA_002109545.1) <em>Perca</em> <em>fluviatilis</em> (GCA_010015445.1), <em>Gasterosteus</em> <em>aculeatus</em> (GCA_016920845.1), <em>Betta</em> <em>splendens</em> (GCA_900634795.3), <em>Acanthopagrus</em> <em>latus</em> (GCA_904848185.1) The predicted proteins were functionally annotated with InterProScan and BlastP against the Swiss-Prot database. Annotation files: H_lanceolatus_GeMoMa_all.fun.gff H_lanceolatus_GeMoMa_proteins.fun.fasta H_lanceolatus_GeMoMa_CDS.fun.fasta H_lanceolatus_GeMoMa_summary All commands used to generate the assembly, the annotation, and additional analyses are listed in the protocol file: H_lanceolatus_assembly_commands.txt