DOI: 10.7291/d1x10b
title: Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific

description: Holacanthus angelfishes are some of the most iconic marine fishes of the
 Tropical Eastern Pacific (TEP). However, very limited genomic resources
 currently exist for the genus. In this study we: i) assembled and
 annotated the nuclear genome of the King Angelfish (Holacanthus passer),
 and ii) examined the demographic history of H. passer in the TEP. We
 generated 43.8 Gb of ONT and 97.3 Gb Illumina reads representing 75X and
 167X coverage, respectively. The final genome assembly size was 583 Mb
 with a contig N50 of 5.7 Mb, which captured 97.5% complete Actinoterygii
 Benchmarking Universal Single-Copy Orthologs (BUSCOs). Repetitive elements
 account for 5.09% of the genome, and 33,889 protein-coding genes were
 predicted, of which 22,984 have been functionally annotated. Our
 demographic model suggests that population expansions of H. passer
 occurred prior to the last glacial maximum (LGM) and were more likely
 shaped by events associated with the closure of the Isthmus of Panama.
 This result is surprising, given that most rapid population expansions in
 both freshwater and marine organisms have been reported to occur globally
 after the LGM. Overall, this annotated genome assembly will serve as a
 resource to improve our understanding of the evolution of Holacanthus
 angelfishes while facilitating novel research into local adaptation,
 speciation, and introgression in marine fishes.
description: To annotate our genome, we
 used the homology-based gene prediction pipeline GeMoMa (v1.6.4). GeMoMa
 uses protein-coding gene models and intron position conservation from
 reference genomes to predict possible protein-coding genes in a target
 genome (Keilwagen et al., 2018). Here, we ran the GeMoMa pipeline using
 annotations from three fish species: <em>Amphiprion ocellaris,
 Oreocromis niloticus, Electrophorus electricus</em> (downloaded from
 NCBI, see Table S3). These species were selected to represent a variety of
 genes from close to distant high-quality fish annotations. In our
 particular case, the pipeline performed four main steps: 1) Extractor or
 external search, using the search algorithm tbalstn with cds parts as
 queries from our reference genomes, 2) Gene Model Mapper (GeMoMa), which
 builds gene models from the extractor results, 3) GeMoMa Annotation Filter
 (GAF) that filters and combines common gene predictions and 4)
 AnnotationFinalizer, which predicts UTRs for annotated coding sequences
 and generate genes and transcripts names (Keilwagen et al., 2018).
 Additionally, repetitive elements were predicted by running RepeatMasker
 (open-4.0.6, Smit et al. 2013–2015) with the Teleostei database to
 identify repetitive elements in the genome and soft-mask the assembly.
 RepeatMasker.out was converted to GFF with RepeatMasker script
 `rmOutToGFF3.pl`.
description: # Whole genome assembly and annotation of the King Angelfish (*Holacanthus
 passer*) gives insight into the evolution of marine fishes of the Tropical
 Eastern Pacific by Remy Gatins, Carlos F. Arias, Carlos Sánchez, Giacomo
 Bernardi, and Luis F. De León corresponding author: remygatinsa@gmail.com
 *** ## Genome Assembly Files * HPA\_1.1.fasta - fasta genome assembly file
 ## Genome Annotation Files * HPA\_1.1\_annotation.gff - gff genome
 annotation file * HPA\_1.1\_nucleotide\_proteins.fasta - coding gene
 nucleotide sequences in fasta file format *
 HPA\_1.1\_predicted\_proteins.fasta - predicted proteins in fasta file
 format * gemoma.job - sbatch job submission to run Gemoma pipeline *
 gemoma\_HPA\_1.1.log - output log file from gemoma.job submission *
 protocol\_GeMoMaPipeline.txt - Gemoma pipeline parameter description ###
 RepeatMasker files * HPA\_04\_pilonb.fasta.cat.gz - alignment file *
 HPA\_04\_pilonb.fasta.masked - fasta file showing repeats across the
 genome * HPA\_04\_pilonb.fasta.out - annotation file with the cross\_match
 output lines * HPA\_04\_pilonb.fasta.tbl - repeatmasker summary file *
 repeatmasker.log - HPA\_repeatmasker log file * repeatmasker.job -
 repeatmasker job sumission ## BUSCO output files *
 missing\_busco\_list\_HPA\_1.1\_busco\_actinopterygii.txt - missing BUSCO
 list using Actinopterygii\_odb9 database *
 missing\_busco\_list\_HPA\_1.1\_busco\_eukaryota.txt - missing BUSCO list
 using Eukaryota\_odb9 database *
 short\_summary\_HPA\_1.1\_busco\_actinopterygii.txt - BUSCO short summary
 using Actinopterygii\_odb9 database *
 short\_summary\_HPA\_1.1\_busco\_eukaryota.txt - BUSCO short summary using
 Eukaryota\_odb9 database *
 full\_table\_HPA\_1.1\_busco\_actinopterygii.tsv - BUSCO full output table
 using Actinopterygii\_odb9 database *
 full\_table\_HPA\_1.1\_busco\_eukaryota.tsv - BUSCO full output table
 using Eukaryota\_odb9 database ## Extra files * HPA\_1.1\_blobtools.zip -
 this zipped folder includes about 40 `.json `files that are used all
 together as input to generate the blob tools viewer.