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. 2022 Oct 21;113(5):568-576.
doi: 10.1093/jhered/esac033.

A Chromosome-Scale Genome Assembly of the Okapi (Okapia johnstoni)

Sven Winter  1   2 , Raphael T F Coimbra  1   3 , Philippe Helsen  4 , Axel Janke  1   5   3
Affiliations

A Chromosome-Scale Genome Assembly of the Okapi (Okapia johnstoni)

Sven Winter et al. J Hered. .

Abstract

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 > 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.

Keywords: 10X Chromium; Giraffidae; Hi-C; PacBio; long-reads.

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Conflict of interest statement

The authors declare that they have no conflicting interests.

Figures

Figure 1.
Figure 1.
The okapi, Hi-C contact map, and Gene set completeness analyses. Painting of the okapi by Jon Baldur Hlidberg (www.fauna.is) (A). Proximity ligation contact map of the scaffolded assembly TBG_Okapi_asm_v1 (B). Gene set completeness analyses (BUSCO) using both the mammalia_odb10 (C) and the cetartiodactyla_odb10 gene sets (D) for the 3 okapi assemblies and the annotation of TBG_Okapi_asm_v1. The assembly with the highest BUSCO scores for both gene sets is TBG_Okapi_asm_v1.
Figure 2.
Figure 2.
Synteny comparison between okapi and other ruminants. Synteny Plot generated with JupiterPlot between the okapi assembly TBG_Okapi_asm_v1 (left) and (A) the okapi assembly ASM166083v1_HiC, (B) Masai giraffe, (C) cattle, and (E) sheep. Boxes in the outer circle of the plot indicate scaffolds of the reference (color) and query (grey). Black lines within the colored boxes represent gaps in the reference assembly.
Figure 3.
Figure 3.
Demographic history of 2 okapi individuals estimated by PSMC.
See this image and copyright information in PMC

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