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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Online Access: | https://researchonline.jcu.edu.au/72406/1/Edwards-2021-Chromosome-length%20genome%20assembly.pdf |
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ftjamescook:oai:researchonline.jcu.edu.au:72406 2024-02-11T10:02:47+01:00 Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome Edwards, Richard J. Field, Matt A. Ferguson, James M. Dudchenko, Olga Keilwagen, Jens Rosen, Benjamin D. Johnson, Gary S. Rice, Edward S. Hillier, La Deanna Hammond, Jillian M. Towarnicki, Samuel G. Omer, Arina Khan, Ruqayya Skvortsova, Ksenia Bogdanovic, Ozren Zammit, Robert A. Aiden, Erez Lieberman Warren, Wesley C. Ballard, J. William O. 2021 application/pdf https://researchonline.jcu.edu.au/72406/1/Edwards-2021-Chromosome-length%20genome%20assembly.pdf unknown BioMed Central https://doi.org/10.1186/s12864-021-07493-6 https://researchonline.jcu.edu.au/72406/ https://researchonline.jcu.edu.au/72406/1/Edwards-2021-Chromosome-length%20genome%20assembly.pdf Edwards, Richard J., Field, Matt A., Ferguson, James M., Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D., Johnson, Gary S., Rice, Edward S., Hillier, La Deanna, Hammond, Jillian M., Towarnicki, Samuel G., Omer, Arina, Khan, Ruqayya, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A., Aiden, Erez Lieberman, Warren, Wesley C., and Ballard, J. William O. (2021) Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics, 22. 188. open Article PeerReviewed 2021 ftjamescook https://doi.org/10.1186/s12864-021-07493-6 2024-01-22T23:50:10Z 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. Article in Journal/Newspaper Canis lupus James Cook University, Australia: ResearchOnline@JCU BMC Genomics 22 1 |
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James Cook University, Australia: ResearchOnline@JCU |
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ftjamescook |
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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 |
Article in Journal/Newspaper |
author |
Edwards, Richard J. Field, Matt A. Ferguson, James M. Dudchenko, Olga Keilwagen, Jens Rosen, Benjamin D. Johnson, Gary S. Rice, Edward S. Hillier, La Deanna Hammond, Jillian M. Towarnicki, Samuel G. Omer, Arina Khan, Ruqayya Skvortsova, Ksenia Bogdanovic, Ozren Zammit, Robert A. Aiden, Erez Lieberman Warren, Wesley C. Ballard, J. William O. |
spellingShingle |
Edwards, Richard J. Field, Matt A. Ferguson, James M. Dudchenko, Olga Keilwagen, Jens Rosen, Benjamin D. Johnson, Gary S. Rice, Edward S. Hillier, La Deanna Hammond, Jillian M. Towarnicki, Samuel G. Omer, Arina Khan, Ruqayya Skvortsova, Ksenia Bogdanovic, Ozren Zammit, Robert A. Aiden, Erez Lieberman Warren, Wesley C. Ballard, J. William O. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
author_facet |
Edwards, Richard J. Field, Matt A. Ferguson, James M. Dudchenko, Olga Keilwagen, Jens Rosen, Benjamin D. Johnson, Gary S. Rice, Edward S. Hillier, La Deanna Hammond, Jillian M. Towarnicki, Samuel G. Omer, Arina Khan, Ruqayya Skvortsova, Ksenia Bogdanovic, Ozren Zammit, Robert A. Aiden, Erez Lieberman Warren, Wesley C. Ballard, J. William O. |
author_sort |
Edwards, Richard J. |
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 |
BioMed Central |
publishDate |
2021 |
url |
https://researchonline.jcu.edu.au/72406/1/Edwards-2021-Chromosome-length%20genome%20assembly.pdf |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_relation |
https://doi.org/10.1186/s12864-021-07493-6 https://researchonline.jcu.edu.au/72406/ https://researchonline.jcu.edu.au/72406/1/Edwards-2021-Chromosome-length%20genome%20assembly.pdf Edwards, Richard J., Field, Matt A., Ferguson, James M., Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D., Johnson, Gary S., Rice, Edward S., Hillier, La Deanna, Hammond, Jillian M., Towarnicki, Samuel G., Omer, Arina, Khan, Ruqayya, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A., Aiden, Erez Lieberman, Warren, Wesley C., and Ballard, J. William O. (2021) Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics, 22. 188. |
op_rights |
open |
op_doi |
https://doi.org/10.1186/s12864-021-07493-6 |
container_title |
BMC Genomics |
container_volume |
22 |
container_issue |
1 |
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1790598835363381248 |