Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes

Abstract

BackgroundThe feline genome is valuable to the veterinary and model organism genomics communities because the cat is an obligate carnivore and a model for endangered felids. The initial public release of the Felis catus genome assembly provided a framework for investigating the genomic basis of feline biology. However, the entire set of protein coding genes has not been elucidated.ResultsWe identified and characterized 1227 protein coding feline sequences, of which 913 map to public sequences and 314 are novel. These sequences have been deposited into NCBI's genbank database and complement public genomic resources by providing additional protein coding sequences that fill in some of the gaps in the feline genome assembly. Through functional and comparative genomic analyses, we gained an understanding of the role of these sequences in feline development, nutrition and health. Specifically, we identified 104 orthologs of human genes associated with Mendelian disorders. We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions. We detected relatively less negative selection on protein sequences encoding extracellular networks, apoptotic pathways and mitochondrial gene ontology annotations. Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes. Together, this analysis provides an overview of the value of our cDNA sequences and enhances our understanding of how the feline genome is similar to, and different from other mammalian genomes.ConclusionsThe cDNA sequences reported here expand existing feline genomic resources by providing high-quality sequences annotated with comparative genomic information providing functional, clinical, nutritional and orthologous gene information.

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly

“…The shared PSGs of Felidae were enriched in polysaccharide binding (GO:0030247, eight genes, P  = 0.00071), lipid binding (GO:0008289, 12 genes, P  = 0.0041), and immune response (GO:0006955, 16 genes, P  = 0.0052; Additional file 3: Table S33). Since felid species are hypercarnivores [3], selection of the lipid binding associated genes may be associated to their obligatory carnivorous diet and regulation of lipid and cholesterol homeostasis [16, 40]. We further identified shared PSGs in the eight carnivores (PSGs in three or more species), five omnivores (PSGs in two or more species), or five herbivores (PSGs in two or more species).…”

The tiger genome and comparative analysis with lion and snow leopard genomes

“…Metabolism pathways associated with protein and fatty acid, which are important sources of energy, were enriched with genes having Panthera -specific functional changes; histidine metabolism ( P =0.00024, Fisher's exact test, six genes), beta-alanine metabolism ( P =0.00078, six genes), phenylalanine metabolism ( P =0.014, three genes), valine, leucine and isoleucine degradation ( P =0.035, six genes), cysteine and methionine metabolism ( P =0.037, four genes), fatty acid metabolism ( P =0.00038, eight genes) and fat digestion and absorption ( P =0.025, five genes) (Supplementary Tables S33 and S34). These signals of amino-acid metabolism have been associated with an obligatory carnivorous diet18.…”

Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes

“…Shared positive selected genes (PSGs) in the Felidae (domestic cat, tiger, lion, cheetah and leopard) are enriched in lipid binding (Kim et al ., ). The selection of lipid binding associated genes may be related to their obligatory carnivorous diet and regulation of lipid and cholesterol homeostasis (Irizarry et al ., ; Cho et al ., ). Our second hypothesis here is that carnivorous carnivorans (CA, especially in hypercarnivorous Felidae and Canidae) may share some PSGs involved in lipid metabolism associated with a hypercarnivorous diet.…”