ICCFGG 2022
#7 Functional annotation of the dog genome Hannes Lohi 1 & DoGA Consortium 2 hannes.lohi@helsinki.fi 1 Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland 2 www.doggenomeannotation.org Unlike other model organisms, the promoter and regulatory regions of the dog genome are not well annotated. To address this issue, we collected fresh tissues (>5000 samples from ~120 tissues) from 14 dogs and four wolves for systematic identification and annotation of transcription starting sites (TSSs), promoters, enhancers, and tissue-specific gene expression. To capture the promoter regions and quantify their expression levels, we generated STRT2 sequencing data from nine dogs, including 482 samples from 88 tissues from 13 organs. We annotated 56,236 robust, ubiquitous and tissue-enriched promoters, of which 36,506 are novel. CAGE-sequencing identified ~55,000 promoters with ~24,000 hitherto unannotated regions and ~21,000 active enhancer regions. We found that ~9,000 promoter and ~12,000 enhancer regions were enriched in a specific tissue. Using the distance and co-expression of promoter and enhancer candidates, we found that 44% of our enhancers are linked to at least one promoter region. Genomic analysis revealed that promoter regions were almost twice as likely to be hit by an SNP compared to other regions in the genome. We compared the sequence of our dog enhancers with human enhancers and found 435 conserved enhancers. Through these efforts, we have established the most comprehensive tissue collection of dogs, a gene expression atlas with a browsable database and interactive platform, and functional annotation of the dog genome with many novel promoters and enhancers. These findings and resources will facilitate the use of the dog as a model for human disease, behavior and morphology. #8 Congenital idiopathic megaesophagus is associated with a variable number tandem repeat in Melanin-Concentrating Hormone Receptor 2 in German Shepherd dogs Jacquelyn M. Evans 1,2 , Sarah M. Bell 1 , Katy M. Evans 3,4 , Kate L. Tsai 1 , Rooksana E. Noorai 1,5 , Thom- as R. Famula 6 , Dolores M. Holle 3 , Leigh Anne Clark 1 jme255@cornell.edu 1 Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA, 2 Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA 3 The Seeing Eye Inc., Morristown, New Jersey, USA, 4 School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK, 5 Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, South Carolina, USA, 6 Department of Animal Science, University of California, Davis, California, USA Congenital idiopathic megaesophagus (CIM) is a genetically complex gastrointestinal motility disorder found across dog breeds but occurring at a uniquely high frequency in the German shepherd dog (GSD). Reduced peristaltic activity and dilation of the esophagus impede the passage of food into the stomach, causing regurgitation of meals upon introduction of solid food. Affected puppies surviving to adulthood require lifelong management and are at risk for aspiration pneumonia. We observed that male GSDs are nearly twice as likely to be affected as females. Using records from a private breeding colony, we show that this bias is independent of body size differenc-
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