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

Irizarry KJ, Malladi SB, Gao X, Mitsouras K, Melendez L, Burris PA, Brockman JA, Al-Murrani SW - BMC Genomics (2012)

Bottom Line: We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions.Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Veterinary Medicine, Western University of Health Sciences, Pomona, California 91766, USA.

ABSTRACT

Background: The 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.

Results: We 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.

Conclusions: The 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.

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Gene Ontology Process Terms by dN/dS Value. A representative sample of gene ontology process terms associated with the proteins encoded by the feline cDNA sequences were stratified by dN/dS values of cat versus dog, human and mouse. The number of feline cDNAs associated with each annotation term is indicated in parentheses.
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Figure 4: Gene Ontology Process Terms by dN/dS Value. A representative sample of gene ontology process terms associated with the proteins encoded by the feline cDNA sequences were stratified by dN/dS values of cat versus dog, human and mouse. The number of feline cDNAs associated with each annotation term is indicated in parentheses.

Mentions: Similar themes were observed within the gene ontology process annotation data. See Figure 4 for a representative map of gene ontology process annotation by dN/dS values. The microtubule theme was represented by the terms microtubule-based process (3 genes, dN/dS = 0), microtubule-based movement (2 genes, dN/dS = 0), cytoskeleton organization (2 genes, dN/dS = 0), microtubule cytoskeleton organization (2 genes, dN/dS = 0), positive regulation of actin filament polymerization (2 genes, dN/dS = 0.01), cytokinesis (4 genes, dN/dS = 0.02), centriole replication (2 genes, dN/dS = 0.02), regulation of cytokinesis (2 genes, dN/dS = 0.02) and actin cytoskeleton organization (9 genes, dN/dS = 0.04). Much like the location annotation, a theme observed in the process annotation related to intracellular transport and included terms such as protein retention in ER lumen (2 genes, dN/dS = 0), calcium ion transport (3 genes, dN/dS = 0.01), golgi to endosome transport (2 genes, dN/dS = 0.01), vesicle docking involved in exocytosis (2 genes, dN/dS = 0.02) and retrograde transport, endosome to Golgi (3 genes, dN/dS = 0.03). Also present, was a protein synthesis/degradation theme supported by the terms proteasomal ubiquitin-dependent protein catabolic process (4 genes, dN/dS = 0.01), post-translational protein modification (7 genes, dN/dS = 0.02), RNA export from nucleus (3 genes, dN/dS = 0.02), protein ubiquination (10 genes, dN/dS = 0.03), translational elongation (15 genes, dN/dS = 0.03) and tRNA aminoacylation for protein translation (4 genes, dN/dS = 0.04). In contrast, process annotation terms exhibiting relatively large dN/dS ratios overlapped with themes of cellular signalling and regulation/response of cells to environmental signals.


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

Irizarry KJ, Malladi SB, Gao X, Mitsouras K, Melendez L, Burris PA, Brockman JA, Al-Murrani SW - BMC Genomics (2012)

Gene Ontology Process Terms by dN/dS Value. A representative sample of gene ontology process terms associated with the proteins encoded by the feline cDNA sequences were stratified by dN/dS values of cat versus dog, human and mouse. The number of feline cDNAs associated with each annotation term is indicated in parentheses.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3278379&req=5

Figure 4: Gene Ontology Process Terms by dN/dS Value. A representative sample of gene ontology process terms associated with the proteins encoded by the feline cDNA sequences were stratified by dN/dS values of cat versus dog, human and mouse. The number of feline cDNAs associated with each annotation term is indicated in parentheses.
Mentions: Similar themes were observed within the gene ontology process annotation data. See Figure 4 for a representative map of gene ontology process annotation by dN/dS values. The microtubule theme was represented by the terms microtubule-based process (3 genes, dN/dS = 0), microtubule-based movement (2 genes, dN/dS = 0), cytoskeleton organization (2 genes, dN/dS = 0), microtubule cytoskeleton organization (2 genes, dN/dS = 0), positive regulation of actin filament polymerization (2 genes, dN/dS = 0.01), cytokinesis (4 genes, dN/dS = 0.02), centriole replication (2 genes, dN/dS = 0.02), regulation of cytokinesis (2 genes, dN/dS = 0.02) and actin cytoskeleton organization (9 genes, dN/dS = 0.04). Much like the location annotation, a theme observed in the process annotation related to intracellular transport and included terms such as protein retention in ER lumen (2 genes, dN/dS = 0), calcium ion transport (3 genes, dN/dS = 0.01), golgi to endosome transport (2 genes, dN/dS = 0.01), vesicle docking involved in exocytosis (2 genes, dN/dS = 0.02) and retrograde transport, endosome to Golgi (3 genes, dN/dS = 0.03). Also present, was a protein synthesis/degradation theme supported by the terms proteasomal ubiquitin-dependent protein catabolic process (4 genes, dN/dS = 0.01), post-translational protein modification (7 genes, dN/dS = 0.02), RNA export from nucleus (3 genes, dN/dS = 0.02), protein ubiquination (10 genes, dN/dS = 0.03), translational elongation (15 genes, dN/dS = 0.03) and tRNA aminoacylation for protein translation (4 genes, dN/dS = 0.04). In contrast, process annotation terms exhibiting relatively large dN/dS ratios overlapped with themes of cellular signalling and regulation/response of cells to environmental signals.

Bottom Line: We detected negative selection within sequences with gene ontology annotations associated with intracellular trafficking, cytoskeleton and muscle functions.Additionally, we characterized feline cDNA sequences that have mouse orthologs associated with clinical, nutritional and developmental phenotypes.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Veterinary Medicine, Western University of Health Sciences, Pomona, California 91766, USA.

ABSTRACT

Background: The 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.

Results: We 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.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus