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Title: Sequencing and genome annotation of honey bee microsporidia parasite, Nosema apis and comparative genome analysis with its sympatric congener, N. ceranae

Author
item Chen, Yanping - Judy
item Pettis, Jeffery
item Zhao, Yan
item Cornman, Robert
item Tallon, Luke - University Of Maryland
item Sadzewicz, Lisa - University Of Maryland
item Ye, Jun - National Institutes Of Health (NIH)
item Li, Ren Hua - National Institutes Of Health (NIH)
item Zhang, Xuan - Yunnan Agricultural University
item Hamilton, Michele
item Pernal, Steven - Agriculture And Agri-Food Canada
item Melathopoulos, Adony - Agriculture And Agri-Food Canada
item Yan, Xianghe
item Evans, Jay

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2013
Publication Date: 7/5/2013
Publication URL: http://handle.nal.usda.gov/10113/57671
Citation: Chen, Y., Pettis, J.S., Zhao, Y., Cornman, R.S., Tallon, L.L., Sadzewicz, L.L., Ye, J., Li, R., Zhang, X., Hamilton, M.C., Pernal, S., Melathopoulos, A., Yan, X., Evans, J.D. 2013. Sequencing and genome annotation of honey bee microsporidia parasite, Nosema apis and comparative genome analysis with its sympatric congener, N. ceranae. Biomed Central (BMC) Genomics. 14:451. DOI: 10.1186/1471-2164-14-451.

Interpretive Summary: The microsporidian parasite Nosema is one of the several suspected factors contributing to the current collapse of honey bee colonies that are essential to our food supply, pollinating approximately $15 billion worth of crops in the U.S. each year. Nosema apis is one of two Nosema species that cause Nosemosis, a serious honey bee disease listed with the Office International des Epizooties (OIE). Here we report analysis of the completed N. apis genome sequence and comparative analysis with N. ceranae, a recent emerging microsporidian parasite of honey bees. Sequencing and annotation of the N. apis genome provide a comprehensive overview of the genetic content, structure, and organization of the parasite and give some interesting insights into the complex biological and molecular processes of the parasite. Comparative genomic analysis of two Nosema species led to identification of genes that are essential for the parasite’s survival and are associated with virulence of the parasites in honey bees. There genes are potential targets for innovative therapeutics to break down the life cycle of the parasite. The results obtained from this study should be of interest to researchers from academia and industry, apiary inspectors, and graduate students in the field of entomology and beekeeping society.

Technical Abstract: Here we present a draft genome sequence and annotation of the honey bee microsporidian parasite, Nosema apis. We applied the whole-genome shotgun (WGS) sequencing approach to sequence and assemble the genome of N. apis to 22-fold sequence coverage. We predicted 2927 protein-coding genes in the N. apis genome which has an estimated size of 8.5 Mbp. Using the Gene Ontology (GO) terms as function labels, we computationally determined how each putative protein functions in biological process, molecular function, and cellular component. Further, we undertook comparative analysis of N. apis protein sequences with that of its sympatric congener, N. ceranae, a fully sequenced microsporidian species. The genome annotations yielded valuable information on the content and architecture of a large microsporidian genome and provide new insight into eukaryotic genome diversity and evolution. The comparative genomic analysis led to the identification of 1241orthologs that are conserved between N. apis and N. ceranae, and genes that are unique characteristics of the individual species, thereby providing a list of virulence factors that are associated with parasite pathogenecity and new genetic tools for studying host-parasite interactions.