Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

doi:10.1186/s12864-021-07493-6

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	Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
	Edwards, Richard J.1; Field, Matt A.2,3; Ferguson, James M.4; Dudchenko, Olga 5,6,7; Keilwagen, Jens 8; Rosen, Benjamin D.9; Johnson, Gary S.10; Rice, Edward S.11; Hillier, La Deanna 12; Hammond, Jillian M.4; Towarnicki, Samuel G.1; Omer, Arina 5,6; Khan, Ruqayya 5,6; Skvortsova, Ksenia 13,14; Bogdanovic, Ozren 1,13; Zammit, Robert A.15; Aiden, Erez Lieberman5,6,7,16,17 ; Warren, Wesley C.18; Ballard, J. William O.19,20
	2021
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	22 期号:1
DOI	10.1186/s12864-021-07493-6
摘要	BackgroundBasenjis 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.ResultsHere, 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.ConclusionsThe 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.
关键词	Canine genome Domestication Comparative genomics Artificial selection
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收录类别	SCIE
语种	英语
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:000630096300004
出版者	BMC
原始文献类型	Article
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/126160
专题	免疫化学研究所_特聘教授组_结构生物化学实验室
通讯作者	Aiden, Erez Lieberman; Warren, Wesley C.; Ballard, J. William O.
作者单位	1.Univ New South Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia; 2.James Cook Univ, Australian Inst Trop Hlth & Med, Ctr Trop Bioinformat & Mol Biol, Cairns, Qld 4878, Australia; 3.Australian Natl Univ, John Curtin Sch Med Res, Canberra, ACT 2600, Australia; 4.Garvan Inst Med Res, Kinghorn Ctr Clin Genom, Victoria St, Darlinghurst, NSW 2010, Australia; 5.Baylor Coll Med, Dept Mol & Human Genet, Ctr Genome Architecture, Houston, TX 77030 USA; 6.Rice Univ, Dept Comp Sci, Houston, TX USA; 7.Rice Univ, Ctr Theoret & Biol Phys, Houston, TX USA; 8.Julius Kuhn Inst, Erwin Baur Str 27, D-06484 Quedlinburg, Germany; 9.ARS, Anim Genom & Improvement Lab, USDA, Beltsville, MD 20705 USA; 10.Univ Missouri, Dept Vet Pathobiol, Columbia, MO 65211 USA; 11.Univ Missouri, Dept Surg, Columbia, MO 65211 USA; 12.Univ Washington, Genome Sci, Seattle, WA 98195 USA; 13.Garvan Inst Med Res, Genom & Epigenet Div, Victoria St, Darlinghurst, NSW 2010, Australia; 14.Univ New South Wales, Fac Med, St Vincents Clin Sch, Sydney, NSW 2010, Australia; 15.Vineyard Vet Hosp, 703 Windsor Rd, Vineyard, NSW 2765, Australia; 16.Univ Western Australia, UWA Sch Agr & Environm, Fac Sci, Perth, WA 6009, Australia; 17.ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China; 18.Univ Missouri, Dept Anim Sci, Columbia, MO 65211 USA; 19.La Trobe Univ, Dept Ecol Environm & Evolut, Melbourne, Vic 3086, Australia; 20.Univ Melbourne, Sch Biosci, Parkville, Vic 3052, Australia
通讯作者单位	免疫化学研究所
推荐引用方式 GB/T 7714	Edwards, Richard J.,Field, Matt A.,Ferguson, James M.,et al. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome[J]. BMC GENOMICS,2021,22(1).
APA	Edwards, Richard J..,Field, Matt A..,Ferguson, James M..,Dudchenko, Olga.,Keilwagen, Jens.,...&Ballard, J. William O..(2021).Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome.BMC GENOMICS,22(1).
MLA	Edwards, Richard J.,et al."Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome".BMC GENOMICS 22.1(2021).