Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Background: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The incre...
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ftdatacite:10.26181/60dd1c4ea92a7 2023-05-15T15:50:45+02:00 Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome Edwards, RJ Field, MA Ferguson, JM Dudchenko, O Keilwagen, J Rosen, BD Johnson, GS Rice, ES Hillier, LD Hammond, JM Towarnicki, SG Omer, A Khan, R Skvortsova, K Bogdanovic, O Zammit, RA Aiden, EL Warren, WC Ballard, John 2021 https://dx.doi.org/10.26181/60dd1c4ea92a7 https://opal.latrobe.edu.au/articles/journal_contribution/Chromosome-length_genome_assembly_and_structural_variations_of_the_primal_Basenji_dog_Canis_lupus_familiaris_genome/14888562 unknown La Trobe Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Uncategorized Text article-journal Journal contribution ScholarlyArticle 2021 ftdatacite https://doi.org/10.26181/60dd1c4ea92a7 2021-11-05T12:55:41Z Background: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results: Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies. Text Canis lupus DataCite Metadata Store (German National Library of Science and Technology) |
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Uncategorized Edwards, RJ Field, MA Ferguson, JM Dudchenko, O Keilwagen, J Rosen, BD Johnson, GS Rice, ES Hillier, LD Hammond, JM Towarnicki, SG Omer, A Khan, R Skvortsova, K Bogdanovic, O Zammit, RA Aiden, EL Warren, WC Ballard, John Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
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Uncategorized |
description |
Background: Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results: Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions: The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies. |
format |
Text |
author |
Edwards, RJ Field, MA Ferguson, JM Dudchenko, O Keilwagen, J Rosen, BD Johnson, GS Rice, ES Hillier, LD Hammond, JM Towarnicki, SG Omer, A Khan, R Skvortsova, K Bogdanovic, O Zammit, RA Aiden, EL Warren, WC Ballard, John |
author_facet |
Edwards, RJ Field, MA Ferguson, JM Dudchenko, O Keilwagen, J Rosen, BD Johnson, GS Rice, ES Hillier, LD Hammond, JM Towarnicki, SG Omer, A Khan, R Skvortsova, K Bogdanovic, O Zammit, RA Aiden, EL Warren, WC Ballard, John |
author_sort |
Edwards, RJ |
title |
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
title_short |
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
title_full |
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
title_fullStr |
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
title_full_unstemmed |
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
title_sort |
chromosome-length genome assembly and structural variations of the primal basenji dog (canis lupus familiaris) genome |
publisher |
La Trobe |
publishDate |
2021 |
url |
https://dx.doi.org/10.26181/60dd1c4ea92a7 https://opal.latrobe.edu.au/articles/journal_contribution/Chromosome-length_genome_assembly_and_structural_variations_of_the_primal_Basenji_dog_Canis_lupus_familiaris_genome/14888562 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.26181/60dd1c4ea92a7 |
_version_ |
1766385765778980864 |