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

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 i...

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Autores principales: Winter, Sven, Coimbra, Raphael T F, Helsen, Philippe, Janke, Axel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9584810/
https://www.ncbi.nlm.nih.gov/pubmed/35788365
http://dx.doi.org/10.1093/jhered/esac033
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author Winter, Sven
Coimbra, Raphael T F
Helsen, Philippe
Janke, Axel
author_facet Winter, Sven
Coimbra, Raphael T F
Helsen, Philippe
Janke, Axel
author_sort Winter, Sven
collection PubMed
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 > 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.
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spelling pubmed-95848102022-10-24 A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni) Winter, Sven Coimbra, Raphael T F Helsen, Philippe Janke, Axel J Hered Genome Resources 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. Oxford University Press 2022-07-05 /pmc/articles/PMC9584810/ /pubmed/35788365 http://dx.doi.org/10.1093/jhered/esac033 Text en © The American Genetic Association. 2022. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Genome Resources
Winter, Sven
Coimbra, Raphael T F
Helsen, Philippe
Janke, Axel
A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)
title A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)
title_full A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)
title_fullStr A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)
title_full_unstemmed A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)
title_short A Chromosome-Scale Genome Assembly of the Okapi (Okapia Johnstoni)
title_sort chromosome-scale genome assembly of the okapi (okapia johnstoni)
topic Genome Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9584810/
https://www.ncbi.nlm.nih.gov/pubmed/35788365
http://dx.doi.org/10.1093/jhered/esac033
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