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

BMC Genomics

Research Article

Kristopher J Irizarry¹  Patricia A Burris²  Sukhaswami B Malladi²  Lynda Melendez²  Jeffrey A Brockman²  Xiangming Gao²  Samer W Al-Murrani²  Katherine Mitsouras³ 

[1] College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, 91766, Pomona, California, USA;The Applied Genomics Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, 91766, Pomona, California, USA;Pet Hill's Pet Nutrition, Pet Nutrition Center, 1035 NE 43rd Street, 66617, Topeka, KS, USA;The Applied Genomics Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, 91766, Pomona, California, USA;College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 91766, Pomona, California, USA;

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

DOI  :  10.1186/1471-2164-13-31

 received in 2011-04-20, accepted in 2012-01-18,  发布年份 2012

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Irizarry et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.