Open Access Highly Accessed Research article

Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions

Yan ping Chen1*, Jeffery S Pettis1, Yan Zhao2, Xinyue Liu3, Luke J Tallon3, Lisa D Sadzewicz3, Renhua Li4, Huoqing Zheng5, Shaokang Huang6, Xuan Zhang7, Michele C Hamilton1, Stephen F Pernal8, Andony P Melathopoulos8, Xianghe Yan9 and Jay D Evans1

Author Affiliations

1 USDA-ARS Bee Research Laboratory, Building 476 BARC-East, Beltsville, MD 20705, USA

2 USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA

3 The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21202, USA

4 Windber Research Institute, 620 7th Street, Windber, PA 15963, USA

5 College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China

6 College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, P.R. China

7 Eastern Bee Research Institute of Yunnan Agriculture University, Kunming, Yunnan 650201, P.R. China

8 Agriculture & Agri-Food Canada, Beaverlodge Research Farm, Beaverlodge, AB, Canada

9 The Molecular Characterization of Foodborne Pathogens Unit, Eastern Regional Research Center (ERRC), Wyndmoor, PA 19038, USA

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BMC Genomics 2013, 14:451  doi:10.1186/1471-2164-14-451

Published: 5 July 2013



The microsporidia parasite Nosema contributes to the steep global decline of honey bees that are critical pollinators of food crops. There are two species of Nosema that have been found to infect honey bees, Nosema apis and N. ceranae. Genome sequencing of N. apis and comparative genome analysis with N. ceranae, a fully sequenced microsporidia species, reveal novel insights into host-parasite interactions underlying the parasite infections.


We applied the whole-genome shotgun sequencing approach to sequence and assemble the genome of N. apis which has an estimated size of 8.5 Mbp. We predicted 2,771 protein- coding genes and predicted the function of each putative protein using the Gene Ontology. The comparative genomic analysis led to identification of 1,356 orthologs that are conserved between the two Nosema species and genes that are unique characteristics of the individual species, thereby providing a list of virulence factors and new genetic tools for studying host-parasite interactions. We also identified a highly abundant motif in the upstream promoter regions of N. apis genes. This motif is also conserved in N. ceranae and other microsporidia species and likely plays a role in gene regulation across the microsporidia.


The availability of the N. apis genome sequence is a significant addition to the rapidly expanding body of microsprodian genomic data which has been improving our understanding of eukaryotic genome diversity and evolution in a broad sense. The predicted virulent genes and transcriptional regulatory elements are potential targets for innovative therapeutics to break down the life cycle of the parasite.

Microsporidia; Nosema; Honey bees; Genome; Comparative genomics