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.### 背景 巴辛吉犬（Basenji）是起源于中非的古老犬种，至今仍与非洲刚果地区的部落民众一同狩猎生活。该犬种因不会吠叫而被称为“无吠犬”，拥有独特的系统发育特征、地理起源与表型性状，使其基因组结构成为研究热点。当前可获取的犬科参考基因组数量持续增长，这使得我们能够探究参考基因组的选择对参考基因组质量及犬品种亲缘关系分析的影响。 ### 结果 本研究报道了两套高质量的巴辛吉犬从头（de novo）基因组组装结果：分别来自雌性个体China（组装版本命名为CanFam_Bas）与雄性个体Wags。我们对巴辛吉犬（CanFam_Bas）、拳师犬（CanFam3.1）以及德国牧羊犬（German Shepherd Dog, GSD，组装版本为CanFam_GSD）三个犬种的组装基因组进行了两两比对，并分析了其间的结构变异。在基因组连续性方面，CanFam_Bas优于CanFam3.1，整体质量与高质量的CanFam_GSD组装结果相当。我们将来自58个代表性犬种的短读长测序数据比对至三套参考基因组，结果证实参考基因组的选择会显著影响读段比对与变异检测的效果。 ### 结论 随着高质量犬科参考基因组数量不断增加，在后续犬科变异分析中，参考基因组的选择已成为愈发关键的决策步骤。巴辛吉犬的基部系统发育地位使其适用于特定犬品种的靶向变异分析。但我们认为，针对整个犬科类群的全面分析，更适合采用泛基因组（pangenome）策略。综上，本研究凸显了在所有变异研究中，参考基因组的选择所具有的重要意义。