Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera
1 USDA-ARS, Bee Research Laboratory, 10300 Baltimore Ave., Beltsville, MD 20705 USA
2 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742 USA
3 Department of Entomology, Texas A&M University, College Station, TX 77843 USA
4 Department of Entomology, Purdue University, West Lafayette, IN 47907 USA
5 USDA-ARS, Honey Bee Research Laboratory, 1157 Ben Hur Rd., Baton Rouge, LA 70820 USA
6 Department of Biology, Georgetown University, 37th and O Streets, NW, Washington, DC 20057 USA
7 CSIRO Entomology, Black Mountain Laboratories, Clunies Ross Street, Black Mountain ACT 2601, Australia
8 Department of Entomology, Penn State University, University Park, PA 16802 USA
BMC Genomics 2010, 11:602 doi:10.1186/1471-2164-11-602Published: 25 October 2010
The ectoparasitic mite Varroa destructor has emerged as the primary pest of domestic honey bees (Apis mellifera). Here we present an initial survey of the V. destructor genome carried out to advance our understanding of Varroa biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of Varroa-Apis interactions and defines the challenges ahead for a comprehensive Varroa genome project.
The genome size was estimated by flow cytometry to be 565 Mbp, larger than most sequenced insects but modest relative to some other Acari. Genomic DNA pooled from ~1,000 mites was sequenced to 4.3× coverage with 454 pyrosequencing. The 2.4 Gbp of sequencing reads were assembled into 184,094 contigs with an N50 of 2,262 bp, totaling 294 Mbp of sequence after filtering. Genic sequences with homology to other eukaryotic genomes were identified on 13,031 of these contigs, totaling 31.3 Mbp. Alignment of protein sequence blocks conserved among V. destructor and four other arthropod genomes indicated a higher level of sequence divergence within this mite lineage relative to the tick Ixodes scapularis. A number of microbes potentially associated with V. destructor were identified in the sequence survey, including ~300 Kbp of sequence deriving from one or more bacterial species of the Actinomycetales. The presence of this bacterium was confirmed in individual mites by PCR assay, but varied significantly by age and sex of mites. Fragments of a novel virus related to the Baculoviridae were also identified in the survey. The rate of single nucleotide polymorphisms (SNPs) in the pooled mites was estimated to be 6.2 × 10-5per bp, a low rate consistent with the historical demography and life history of the species.
This survey has provided general tools for the research community and novel directions for investigating the biology and control of Varroa mites. Ongoing development of Varroa genomic resources will be a boon for comparative genomics of under-represented arthropods, and will further enhance the honey bee and its associated pathogens as a model system for studying host-pathogen interactions.