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Open Access Research article

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

Kristopher J Irizarry12, Sukhaswami B Malladi3, Xiangming Gao3, Katherine Mitsouras24, Lynda Melendez3, Patricia A Burris3, Jeffrey A Brockman3 and Samer W Al-Murrani3*

Author affiliations

1 College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street Pomona California, 91766, USA

2 The Applied Genomics Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona California 91766, USA

3 Pet Hill's Pet Nutrition, Pet Nutrition Center, 1035 NE 43rd Street Topeka, KS 66617, USA

4 College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona California 91766, USA

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Citation and License

BMC Genomics 2012, 13:31  doi:10.1186/1471-2164-13-31

Published: 18 January 2012

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.

Keywords:
Feline; bioinformatics; comparative genomics; cDNA; annotation; gene ontology; OMIM; ortholog; nutrition; phenotype