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A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert

Farré, Marta, Li, Qiye, Zhou, Yang, Damas, Joana, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Zhang, Guojie, Larkin, Denis M, and others. (2019) A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. GigaScience, 8 (2). Article Number 162. ISSN 2047-217X. (doi:10.1093/gigascience/giy162) (KAR id:73457)

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https://doi.org/10.1093/gigascience/giy162

Abstract

Background

Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions.

Conclusions

Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.

Item Type: Article
DOI/Identification number: 10.1093/gigascience/giy162
Uncontrolled keywords: gemsbok; Oryx gazella; assembly; annotation; ruminant; drought
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
Depositing User: Marta Farre Belmonte
Date Deposited: 11 Apr 2019 11:07 UTC
Last Modified: 05 Oct 2020 14:30 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/73457 (The current URI for this page, for reference purposes)
Farré, Marta: https://orcid.org/0000-0001-9170-5767
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