Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera

Cornman, S. R., Schatz, M. C., Johnston, S. J., Chen, Y., Pettis, J., Hunt, G., Bourgeois, L., Elsik, C., Anderson, D., Grozinger, C. M., Evans, J. D. (2010) Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. BMC Genomics, 11 (1). ISSN 14712164 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/20973996
DOI: 10.1186/1471-2164-11-602

Abstract

Background: 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.Results: 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.Conclusions: 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. © 2010 Cornman et al; licensee BioMed Central Ltd.

Item Type: Paper
Uncontrolled Keywords: genomic DNA microsatellite DNA Actinomycetales amino acid sequence arthropod article Baculovirus eukaryote gene identification gene sequence genetic analysis genome size honeybee host parasite interaction Ixodes scapularis nonhuman nucleotide sequence population genetics pyrosequencing sequence homology single nucleotide polymorphism Varroa Actinobacteria animal bee codon contig mapping DNA base composition DNA sequence gene locus genetics genome microbiology molecular evolution molecular genetics open reading frame parasite parasitology Varroidae Acari Apis Apis mellifera Arthropoda Bacteria (microorganisms) Baculoviridae Eukaryota Hexapoda Ixodida Varroa destructor Animals Base Composition Bees Evolution, Molecular Genetic Loci Microsatellite Repeats Molecular Sequence Annotation Open Reading Frames Parasites Polymorphism, Single Nucleotide Sequence Analysis DNA
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
organism description > animal > insect
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: CSHL Librarian
Date: 2010
Date Deposited: 16 Mar 2012 14:45
Last Modified: 15 Mar 2013 19:03
PMCID: PMC3091747
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25363

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