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Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked long reads

Ellie E Armstrong, Ryan W. Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza, John Steulpnagel, Claudio Sillero-Zubiri, View ORCID ProfileDmitri Petrov
doi: https://doi.org/10.1101/195180
Ellie E Armstrong
Stanford University;
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  • For correspondence: elliea@stanford.edu
Ryan W. Taylor
Stanford University;
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Stefan Prost
Stanford University;
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Peter Blinston
Painted Dog Conservation;
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Esther van der Meer
Painted Dog Conservation;
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Hillary Madzikanda
Painted Dog Conservation;
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Olivia Mufute
The Zimbabwe Parks & Wildlife Management Authority;
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Roseline Mandisodza
The Zimbabwe Parks & Wildlife Management Authority;
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John Steulpnagel
10x Genomics, Inc.;
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Claudio Sillero-Zubiri
University of Oxford
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Dmitri Petrov
Stanford University;
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Abstract

A high-quality reference genome assembly is a valuable tool for the study of non-model organisms across disciplines. Genomic techniques can provide important insights about past population sizes, local adaptation, and even aid in the development of breeding management plans. This information can be particularly important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets. Here we report the generation of high-quality reference genomes for the African wild dog (Lycaon pictus) at a low cost, thereby facilitating future studies of this endangered canid. We generated assemblies for three individuals from whole blood samples using the linked-read 10x Genomics Chromium system. The most continuous assembly had a scaffold N50 of 21 Mb, a contig N50 of 83 Kb, and completely reconstructed 95% of conserved mammalian genes as reported by BUSCO v2, indicating a high assembly quality. Thus, we show that 10x Genomics Chromium data can be used to effectively generate high-quality genomes of mammal species from Illumina short-read data of intermediate coverage (~25-50x). Interestingly, the African wild dog shows a much higher heterozygosity than other species of conservation concern, possibly as a result of its behavioral ecology. The availability of reference genomes for non-model organisms will facilitate better genetic monitoring of threatened species such as the African wild dog. At the same time, they can help researchers and conservationists to better understand the ecology and adaptability of those species in a changing environment.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 27, 2017.
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Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked long reads
Ellie E Armstrong, Ryan W. Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza, John Steulpnagel, Claudio Sillero-Zubiri, Dmitri Petrov
bioRxiv 195180; doi: https://doi.org/10.1101/195180
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Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked long reads
Ellie E Armstrong, Ryan W. Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza, John Steulpnagel, Claudio Sillero-Zubiri, Dmitri Petrov
bioRxiv 195180; doi: https://doi.org/10.1101/195180

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