Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Abstract 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. T...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BMC
2021
|
Subjects: | |
Online Access: | https://doi.org/10.1186/s12864-021-07493-6 https://doaj.org/article/6ff5d0c6b0d648a3a470a79f1540a8d8 |
id |
ftdoajarticles:oai:doaj.org/article:6ff5d0c6b0d648a3a470a79f1540a8d8 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:6ff5d0c6b0d648a3a470a79f1540a8d8 2023-05-15T15:50:51+02:00 Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome Richard J. Edwards Matt A. Field James M. Ferguson Olga Dudchenko Jens Keilwagen Benjamin D. Rosen Gary S. Johnson Edward S. Rice La Deanna Hillier Jillian M. Hammond Samuel G. Towarnicki Arina Omer Ruqayya Khan Ksenia Skvortsova Ozren Bogdanovic Robert A. Zammit Erez Lieberman Aiden Wesley C. Warren J. William O. Ballard 2021-03-01T00:00:00Z https://doi.org/10.1186/s12864-021-07493-6 https://doaj.org/article/6ff5d0c6b0d648a3a470a79f1540a8d8 EN eng BMC https://doi.org/10.1186/s12864-021-07493-6 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-021-07493-6 1471-2164 https://doaj.org/article/6ff5d0c6b0d648a3a470a79f1540a8d8 BMC Genomics, Vol 22, Iss 1, Pp 1-19 (2021) Canine genome Domestication Comparative genomics Artificial selection Biotechnology TP248.13-248.65 Genetics QH426-470 article 2021 ftdoajarticles https://doi.org/10.1186/s12864-021-07493-6 2022-12-31T07:03:04Z Abstract 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 Directory of Open Access Journals: DOAJ Articles BMC Genomics 22 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Canine genome Domestication Comparative genomics Artificial selection Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Canine genome Domestication Comparative genomics Artificial selection Biotechnology TP248.13-248.65 Genetics QH426-470 Richard J. Edwards Matt A. Field James M. Ferguson Olga Dudchenko Jens Keilwagen Benjamin D. Rosen Gary S. Johnson Edward S. Rice La Deanna Hillier Jillian M. Hammond Samuel G. Towarnicki Arina Omer Ruqayya Khan Ksenia Skvortsova Ozren Bogdanovic Robert A. Zammit Erez Lieberman Aiden Wesley C. Warren J. William O. Ballard Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome |
topic_facet |
Canine genome Domestication Comparative genomics Artificial selection Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract 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 |
Richard J. Edwards Matt A. Field James M. Ferguson Olga Dudchenko Jens Keilwagen Benjamin D. Rosen Gary S. Johnson Edward S. Rice La Deanna Hillier Jillian M. Hammond Samuel G. Towarnicki Arina Omer Ruqayya Khan Ksenia Skvortsova Ozren Bogdanovic Robert A. Zammit Erez Lieberman Aiden Wesley C. Warren J. William O. Ballard |
author_facet |
Richard J. Edwards Matt A. Field James M. Ferguson Olga Dudchenko Jens Keilwagen Benjamin D. Rosen Gary S. Johnson Edward S. Rice La Deanna Hillier Jillian M. Hammond Samuel G. Towarnicki Arina Omer Ruqayya Khan Ksenia Skvortsova Ozren Bogdanovic Robert A. Zammit Erez Lieberman Aiden Wesley C. Warren J. William O. Ballard |
author_sort |
Richard J. Edwards |
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 |
BMC |
publishDate |
2021 |
url |
https://doi.org/10.1186/s12864-021-07493-6 https://doaj.org/article/6ff5d0c6b0d648a3a470a79f1540a8d8 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
BMC Genomics, Vol 22, Iss 1, Pp 1-19 (2021) |
op_relation |
https://doi.org/10.1186/s12864-021-07493-6 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-021-07493-6 1471-2164 https://doaj.org/article/6ff5d0c6b0d648a3a470a79f1540a8d8 |
op_doi |
https://doi.org/10.1186/s12864-021-07493-6 |
container_title |
BMC Genomics |
container_volume |
22 |
container_issue |
1 |
_version_ |
1766385880158699520 |