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

Cornman SR, Schatz MC, Johnston SJ, Chen YP, Pettis J, Hunt G, Bourgeois L, Elsik C, Anderson D, Grozinger CM, Evans JD - BMC Genomics (2010)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA-ARS, Bee Research Laboratory, 10300 Baltimore Ave., Beltsville, MD 20705, USA.

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 × 10-5 per 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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2C genome size estimate for Varroa destructor. 2C genome size estimate for V. destructor based on flow cytometry, normalized to the Drosophila virilis genome (A). The V. destructor fluorescence peak (B) corresponds to a genome size of 0.577 picograms or 565 ± 3 Mbp.
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Figure 1: 2C genome size estimate for Varroa destructor. 2C genome size estimate for V. destructor based on flow cytometry, normalized to the Drosophila virilis genome (A). The V. destructor fluorescence peak (B) corresponds to a genome size of 0.577 picograms or 565 ± 3 Mbp.

Mentions: Flow cytometry of V. destructor nuclei (normalized to nuclei of Drosophila virilis) yielded a haploid genome size estimate of 565 ± 3 Mbp (Figure 1). This genome size is larger than that of many insects but substantially smaller than that of numerous mites and ticks for which genome projects are underway or have been proposed (> 2,000 Mbp, [26]. It is also lower than the general range for ticks, which spans from roughly 1,000 Mbp in the argasid soft tick Ornithodoros turicata to 3,100 Mb in the ixodid hard tick Amblyomma americanum [27]. However, examples of very small acarid genomes are known. Most notably, the two-spotted spider mite Tetranychus urticae, which has been advocated as a model for genetic and developmental studies of chelicerates [28]), has an estimated genome size of only 75 Mbp. It is not yet clear to what extent these large differences in genome size are driven by variation in gene content, repetitive fraction, and/or ploidy. While the contributions of the latter two factors have been frequently noted, the potential contribution of gene expansion has been highlighted by recent analyses of waterflea [29] and pea aphid [30]that reveal a roughly two-fold increase in gene content relative to other arthropods.


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

Cornman SR, Schatz MC, Johnston SJ, Chen YP, Pettis J, Hunt G, Bourgeois L, Elsik C, Anderson D, Grozinger CM, Evans JD - BMC Genomics (2010)

2C genome size estimate for Varroa destructor. 2C genome size estimate for V. destructor based on flow cytometry, normalized to the Drosophila virilis genome (A). The V. destructor fluorescence peak (B) corresponds to a genome size of 0.577 picograms or 565 ± 3 Mbp.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091747&req=5

Figure 1: 2C genome size estimate for Varroa destructor. 2C genome size estimate for V. destructor based on flow cytometry, normalized to the Drosophila virilis genome (A). The V. destructor fluorescence peak (B) corresponds to a genome size of 0.577 picograms or 565 ± 3 Mbp.
Mentions: Flow cytometry of V. destructor nuclei (normalized to nuclei of Drosophila virilis) yielded a haploid genome size estimate of 565 ± 3 Mbp (Figure 1). This genome size is larger than that of many insects but substantially smaller than that of numerous mites and ticks for which genome projects are underway or have been proposed (> 2,000 Mbp, [26]. It is also lower than the general range for ticks, which spans from roughly 1,000 Mbp in the argasid soft tick Ornithodoros turicata to 3,100 Mb in the ixodid hard tick Amblyomma americanum [27]. However, examples of very small acarid genomes are known. Most notably, the two-spotted spider mite Tetranychus urticae, which has been advocated as a model for genetic and developmental studies of chelicerates [28]), has an estimated genome size of only 75 Mbp. It is not yet clear to what extent these large differences in genome size are driven by variation in gene content, repetitive fraction, and/or ploidy. While the contributions of the latter two factors have been frequently noted, the potential contribution of gene expansion has been highlighted by recent analyses of waterflea [29] and pea aphid [30]that reveal a roughly two-fold increase in gene content relative to other arthropods.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA-ARS, Bee Research Laboratory, 10300 Baltimore Ave., Beltsville, MD 20705, USA.

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 × 10-5 per 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.

Show MeSH
Related in: MedlinePlus