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

Scott R. Cornman, Michael C. Schatz, Spencer J. Johnston, Yan Ping Chen, Jeff Pettis, Greg Hunt, Lanie Bourgeois, Chris Elsik, Denis Anderson, Christina M. Grozinger, Jay D. Evans

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Article number602
JournalBMC genomics
Volume11
Issue number1
DOIs
StatePublished - Oct 25 2010

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Varroidae
Honey
Mites
Bees
Tick Control
Genome
Arthropods
Actinomycetales
Host-Pathogen Interactions
Surveys and Questionnaires
Genome Size
Ixodes
Conserved Sequence
Sequence Alignment
Baculoviridae
Population Genetics
Ticks
Sequence Homology
Genomics
Single Nucleotide Polymorphism

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Cornman, S. R., Schatz, M. C., Johnston, S. J., Chen, Y. P., Pettis, J., Hunt, G., ... 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), [602]. https://doi.org/10.1186/1471-2164-11-602
Cornman, Scott R. ; Schatz, Michael C. ; Johnston, Spencer J. ; Chen, Yan Ping ; Pettis, Jeff ; Hunt, Greg ; Bourgeois, Lanie ; Elsik, Chris ; Anderson, Denis ; Grozinger, Christina M. ; Evans, Jay D. / Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. In: BMC genomics. 2010 ; Vol. 11, No. 1.
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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.",
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Cornman, SR, Schatz, MC, Johnston, SJ, Chen, YP, Pettis, J, Hunt, G, Bourgeois, L, Elsik, C, Anderson, D, Grozinger, CM & Evans, JD 2010, 'Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera', BMC genomics, vol. 11, no. 1, 602. https://doi.org/10.1186/1471-2164-11-602

Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. / Cornman, Scott R.; Schatz, Michael C.; Johnston, Spencer J.; Chen, Yan Ping; Pettis, Jeff; Hunt, Greg; Bourgeois, Lanie; Elsik, Chris; Anderson, Denis; Grozinger, Christina M.; Evans, Jay D.

In: BMC genomics, Vol. 11, No. 1, 602, 25.10.2010.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera

AU - Cornman, Scott R.

AU - Schatz, Michael C.

AU - Johnston, Spencer J.

AU - Chen, Yan Ping

AU - Pettis, Jeff

AU - Hunt, Greg

AU - Bourgeois, Lanie

AU - Elsik, Chris

AU - Anderson, Denis

AU - Grozinger, Christina M.

AU - Evans, Jay D.

PY - 2010/10/25

Y1 - 2010/10/25

N2 - 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.

AB - 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.

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