GSD_1.0 (canFam4): A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

Wang, Chao; Wallerman, Ola; Arendt, Maja L.; Sundström, Elisabeth; Karlsson, Åsa; Nordin, Jessika; Mäkeläinen, Suvi; Pielberg, Gerli; Hanson, Jeanette; Ohlsson, Åsa; Saellström, Sara; Rönnberg, Henrik; Ljungvall, Ingrid; Häggström, Jens; Bergström, Tomas F.; Hedhammar, Åke; Meadows, Jennifer R. S.; Lindblad‐Toh, Kerstin

doi:10.21203/rs.3.rs-57997/v1

Cited by 5 publications

(4 citation statements)

References 52 publications

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“…Sequencing and assembly efforts are increasingly moving from species reference genomes to breed-specific assemblies, such as those recently published for Great Dane [ 52 ], Labrador Retriever [ 53 ], and a second GSD [ 54 ]. Together, our data suggest that a single high-quality reference should be sufficient for most general analyses, but the generation of breed-specific genomes is likely to be important for canine nutrition and disease studies.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…Comparison of our Great Dane genome to the CanFam3.1 reference revealed several key findings important to canine genome biology. Several other long-read assemblies of canines are planned or have been recently released (77,78). The availability of these resources will provide significant benefits to the canine genomics community.…”

Section: Discussionmentioning

confidence: 99%

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Halo

Pendleton

Shen

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3′ end of LINE-1_Cfs (i.e., LINE-1_Cf 3′-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.

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“…Moreover, the application of BioNano technologies offers the detection of chromosomal abnormalities, CNVs and structural variants [ 89 ] with a high resolution [ 91 ]. A very recent update of the canine genome reference sequence [ 92 ] should facilitate the successful use of the sequencing technologies. Taken together, it is expected that the spectrum of traditional cytogenetic techniques used in clinical diagnosis will be replaced by advanced DNA-based technologies, which are named “cytogenomics” [ 93 ].…”

Section: Discussionmentioning

confidence: 99%

Clinical Cytogenetics of the Dog: A Review

Szczerbal

Świtoński

2021

Animals

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The dog is an important companion animal and has been recognized as a model in biomedical research. Its karyotype is characterized by a high chromosome number (2n = 78) and by the presence of one-arm autosomes, which are mostly small in size. This makes the dog a difficult subject for cytogenetic studies. However, there are some chromosome abnormalities that can be easily identified, such as sex chromosome aneuploidies, XX/XY leukocyte chimerism, and centric fusions (Robertsonian translocations). Fluorescence in situ hybridization (FISH) with the use of whole-chromosome painting or locus-specific probes has improved our ability to identify and characterize chromosomal abnormalities, including reciprocal translocations. The evaluation of sex chromosome complement is an important diagnostic step in dogs with disorders of sex development (DSD). In such cases, FISH can detect the copy number variants (CNVs) associated with the DSD phenotype. Since cancers are frequently diagnosed in dogs, cytogenetic evaluation of tumors has also been undertaken and specific chromosome mutations for some cancers have been reported. However, the study of meiotic, gamete, and embryo chromosomes is not very advanced. Knowledge of canine genome organization and new molecular tools, such as aCGH (array comparative genome hybridization), SNP (single nucleotide polymorphism) microarray, and ddPCR (droplet digital PCR) allow the identification of chromosomal rearrangements. It is anticipated that the comprehensive use of chromosome banding, FISH, and molecular techniques will substantially improve the diagnosis of chromosome abnormalities in dogs.

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GSD_1.0 (canFam4): A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

Cited by 5 publications

References 52 publications

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

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

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Clinical Cytogenetics of the Dog: A Review

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