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. 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.

Transcript- and annotation-guided genome assembly of the European starling

“…BUSCO assesses the presence or absence of highly conserved lineage-specific genes but is limited to a set of common single-copy genes that may represent easier regions of the genome to sequence and assemble based on current bioinformatics technologies. Furthermore, BUSCO analysis is vulnerable to unpredictable misreporting of presence/completeness for specific genes as a consequence of assembly differences elsewhere in the genome (Edwards et al, 2018;Edwards 2019;Field et al, 2020;Edwards et al, 2021). In addition to the above drawbacks, these methods do not explicitly test the genome assembly's ability to perform the role for which it was intended (e.g., to serve as a reference genome for specific genomic analysis).…”

Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome

“…To date, five long-read-based de novo dog genome assemblies [8][9][10] have been made available at the NCBI genome repository with comparable parameters such as number of genes annotated and number of gaps between the new assemblies. The NCBI has annotated all five genomes and made them available on their genome browser https://www.ncbi.…”

“…AMY2B copy number is variable both within and among modern dog breeds [46], suggesting a dynamic copy number state, perhaps reflecting recurrent expansion and contraction of a tandemly duplicated array. Long-read assembly data from a Basenji, named China [9], and a German Shepherd, named Nala [47], support the presence of a tandemly duplicated architecture at the AMY2B locus. In addition to tandem duplications, large segmental duplications encompassing AMY2B have also been described [26,48].…”

“…Furthermore, high-quality assemblies are an essential prerequisite for accurate annotation, which is required to assay the potential functional effects of detected variants. Recently, several high-quality genomes from different dogs became available [8][9][10].…”

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

“…ONT reads were mapped onto each draft genome using Minimap2 (Minimap2, RRID:SCR_018550) v2.17 [41] (--secondary=no -ax mapont). The single-copy read depth for each assembly was then calculated as the modal read depth across single copy complete BUSCO genes, which should be reasonably robust to poor-quality and/or repeat regions within these genes [42].…”