ICCFGG 2022
#24 Variable representation of duplicated sequence in recent canine genome assemblies
Anthony K. Nguyen and Dr. Jeffrey M. Kidd antnguye@umich.edu University of Michigan, Department of Human Genetics, USA
Gene duplications arise through two means: the reverse transcription and integration of RNA transcripts, or the duplication of DNA segments. DNA-level duplications take the form of either whole genome duplications, or smaller and restricted segmental duplications, which can create ad- ditional copies of genes or gene clusters. Copy number variants (CNVs) refers to the differing copy number of duplications between individuals or populations. These can lead to the evolution of novel gene functions, alterations of normal gene expression patterns, and are associated with a range of adaptive and detrimental phenotypes. Despite the importance of duplications, systematically identifying and analyzing these variants has been challenging. The recent explosion of new canine long-read genome assemblies allows for a finer investigation of duplicated sequences in the canine model than ever before. However, the extent to which duplicated sequences are accurately repre- sented in these new assemblies remains unclear. By conducting genome assembly self-alignment using the computational program BISER, and read depth analysis using fastCN and QuicK-mer2, we have assessed the representation of duplicated genomic sequences in nine published, long-read, high-quality canine genome assemblies. Our analysis has three major conclusions. The first is that retrogenes appear to be proliferating throughout assemblies at high rates with variable levels of representation. The second is that recently published genome assemblies include several nota- bly-misassembled duplications. Finally, some differences between assemblies reflect polymorphic duplications that are segregating among canines. #25 The basis of color pattern development and diversity in cats Christopher B. Kaelin 1,2 , Kelly A. McGowan 1,2 , Brynn M. Brady 1 , Anthony D. Hutcherson 3 , and Gregory S. Barsh 1,2 ckaelin@hudsonalpha.org 1 Department of Genetics, Stanford University, Stanford, CA, USA. 2 HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA. 3 The International Cat Association, Harlingen, Texas, USA Periodic color patterns are a defining aspect of diversity in Felidae. Recent work by our group identified two genes, Taqpep and Dkk4 , that shape pattern type in the domestic cat and other felid species. Variation of color patterns are especially striking in the Bengal cat, a popular breed derived from domestic cat-leopard cat intercrosses and characterized by ornate color patterns not found in other domestic cat breeds. We applied single-cell gene expression and histologic analyses to fetal skin collected from feral cat spay-neuter clinics. We also examined genotype-phenotype associa- tions using genomic DNA and computational analysis of images from 860 Bengal cats, and carried out mixed model associations with either genotypes or species ancestry imputed from low coverage whole genome sequencing. We discovered a pre-pattern of gene expression in embryonic skin from feral cats that corresponds to adult color pattern, and becomes evident prior to hair follicle development, weeks before color patterns are apparent. Embryonic and genetic studies reveal instructive roles for WNT signaling pathway components, including Dkk4, Wnt10b, and Wif1 . Several of the same genes emerge as strong candidates in quantitative trait mapping studies of Bengal
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