title: Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees.
abstract: Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the N. ceranae genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. N. ceranae has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian Encephalitozoon cuniculi, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites. A substantial fraction of the diminutive N. ceranae proteome consists of novel and transposable-element proteins. For a majority of well-supported gene models, a conserved sense-strand motif can be found within 15 bases upstream of the start codon; a previously uncharacterized version of this motif is also present in E. cuniculi. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee-Nosema interactions.
authors.affiliation: USDA-ARS Bee Research Lab, Beltsville, Maryland, United States of America.
authors.forename: R Scott
authors.initials: RS
authors.lastname: Cornman
authors.forename: Yan Ping
authors.initials: YP
authors.lastname: Chen
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
authors.forename: Craig
authors.initials: C
authors.lastname: Street
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Brian
authors.initials: B
authors.lastname: Desany
authors.forename: Michael
authors.initials: M
authors.lastname: Egholm
authors.forename: Stephen
authors.initials: S
authors.lastname: Hutchison
authors.forename: Jeffery S
authors.initials: JS
authors.lastname: Pettis
authors.forename: W Ian
authors.initials: WI
authors.lastname: Lipkin
authors.forename: Jay D
authors.initials: JD
authors.lastname: Evans
mesh_terms: D000818:Animals; D001483:Base Sequence; D001516:Bees / Q000382:microbiology*; D003062:Codon / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D003627:Data Interpretation, Statistical; D009670:Encephalitozoon cuniculi / Q000235:genetics; D005800:Genes, Fungal; D016681:Genome, Fungal; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016818:Nosema / Q000235:genetics* / Q000472:pathogenicity; D050436:Regulatory Elements, Transcriptional / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013172:Spores, Fungal / Q000235:genetics
chemical_list: D003062:Codon