DOI: 10.5061/dryad.37pvmcvp3
title: A chromosome-scale genome assembly of the okapi (Okapia johnstoni)

description: The okapi (Okapia johnstoni), or forest giraffe, is the only species in
 its genus and the only extant sister group of the giraffe within the
 family Giraffidae. The species is one of the remaining large vertebrates
 surrounded by mystery because of its elusive behavior as well as the armed
 conflicts in the region where it occurs, making it difficult to study.
 Deforestation puts the okapi under constant anthropogenic pressure, and it
 is currently listed as “Endangered” on the IUCN Red List. Here, we present
 the first annotated de novo okapi genome assembly based
 on PacBio continuous long reads, polished with short reads, and anchored
 into chromosome-scale scaffolds using Hi-C proximity ligation sequencing.
 The final assembly (TBG_Okapi_asm_v1) has a length of 2.39 Gbp, of which
 98% are represented by 28 scaffolds &gt;3.9 Mbp. The contig N50 of 61
 Mbp and scaffold N50 of 102 Mbp, together with a BUSCO score of 94.7%, and
 23,412 annotated genes, underline the high quality of the assembly. This
 chromosome-scale genome assembly is a valuable resource for future
 conservation of the species and comparative genomic studies among the
 giraffids and other ruminants.
description: Genome assembly:   We assembled the genome of
 the okapi from pacbio CLR reads using WTDBG2 v. 2.5 (Ruan & Li,
 2019) using the preset for PacBio Sequel reads (flag '-x sq')
 followed by three iterations of long-read polishing with racon v.1.4.3
 (Vaser et al., 2017) 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 publically available Hi-C data (SRR8616855,
 SRR8616856).   Subsequently, three iterations of gap-closing were
 performed using TGS-GapCloser v.1.1.1 (Xu et al., 2020). The resulting
 final assembly can be found under the filename: 
 TBG_Okapi_asm_v1.fasta.  Genome
 annotation: Prior to gene annotation, we used
 RepeatModeler v. 2.0.1 for the generation of a de novo repeat library.
 This library was combined with a Cetartiodactyla-specific (Flynn et al.,
 2020) 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). Interspersed repeats were
 hard-masked while simple repeats were soft-masked. The masked assembly
 file can be found under the filename:
 TBG_Okapi_asm_v1_hardmaskedTEs_softmaskedSR.fasta
 After repeat masking we used the GeMoMa pipeline v.1.7.1
 (Keilwagen et al., 2016, 2018) for homology-based gene prediction with the
 alignment tool MMSeqs2 (Steinegger & Söding, 2017).  As references
 we used the assemblies and annotations of the following ten mammals
 species from GenBank: Bos taurus (GCF_002263795.1), Homo sapiens
 (GCF_000001405.39), Mus musculus (GCF_000001635.27), Sus scrofa
 (GCF_000003025.6), Camelus dromedarius (GCF_000803125.2), Equus caballus
 (GCF_002863925.1), Ovis aries (GCF_002742125.1), Tursiops truncatus
 (GCF_011762595.1), Cervus hanglu yarkandensis (GCA_010411085.1), and Capra
 hircus (GCF_001704415.1). Subsequently, the predicted genes were annotated
 by a BLASTP v.2.11.0+ (Zhang et al., 2000) search against the Swiss-Prot
 database (release 2021-01). with an e-value cutoff of 10-6. We further
 annotated Gene ontology terms, motifs, and domains using InterProScan
 v.5.50.84 (Jones et al., 2014; Quevillon et al., 2005). The annotation
 results (gff3, CDS fasta, proteins fasta) can be found under the
 filenames: 
 TBG_Okapi_asm_v1_annotation_all.fun.gff 
 TBG_Okapi_asm_v1_annotation_CDS.fun.fasta
 TBG_Okapi_asm_v1_annotation_proteins.fun.fasta
 For detailed methods and additional results, please read the
 linked publication in the Journal of Heredity.