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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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Evidence that high G+C contigs are bacterial. Contigs with a BLASTX match to the bacterial order Actinomycetales (at an expectation of 10-8 or less), plotted as a function of G+C content and contig length. Points are color-coded according to the taxonomy of the best GenBank match overall. There is a clean separation between contigs with lower G+C that are more similar, by percent identity and expectation of BLASTX sequence alignments, to arthropod sequences and contigs with higher G+C that are more similar to actinomycete sequences.
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Figure 4: Evidence that high G+C contigs are bacterial. Contigs with a BLASTX match to the bacterial order Actinomycetales (at an expectation of 10-8 or less), plotted as a function of G+C content and contig length. Points are color-coded according to the taxonomy of the best GenBank match overall. There is a clean separation between contigs with lower G+C that are more similar, by percent identity and expectation of BLASTX sequence alignments, to arthropod sequences and contigs with higher G+C that are more similar to actinomycete sequences.

Mentions: We then examined G+C content of contigs (Figure 3), which suggested that Varroa nuclear DNA falls largely between 32-58% G+C content (40.9% G+C on average). Contigs with lower G+C content and higher coverage showed strong homology to mitochondrial and ribosomal DNA sequences previously reported for V. destructor, as would be expected. Contigs with higher G+C consistently showed higher sequence similarity to bacterial sequences than to arthropod sequences. For example, Figure 4 illustrates the distribution of contigs with BLASTX matches to the high G+C bacterial order Actinomycetales at an expectation of 10-8, plotted as a function of length and G+C content of contigs. Of these contigs, only those above approximately 58% G+C content were better matches (by sequence similarity and E-value) to Actinomycetales than to arthropods, or lacked an arthropod match entirely. Based on these considerations, we removed contigs outside the range of 32-58% G+C from the analyzed V. destructor assembly unless they contained a superior match to a eukaryotic sequence in GenBank at an expectation of 10-8. Additional filtering was performed as described in the Methods to specifically remove sequences from organisms that were considered potential contaminants a priori, such as known microbial pathogens of honey bees that are dispersed as spores.


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)

Evidence that high G+C contigs are bacterial. Contigs with a BLASTX match to the bacterial order Actinomycetales (at an expectation of 10-8 or less), plotted as a function of G+C content and contig length. Points are color-coded according to the taxonomy of the best GenBank match overall. There is a clean separation between contigs with lower G+C that are more similar, by percent identity and expectation of BLASTX sequence alignments, to arthropod sequences and contigs with higher G+C that are more similar to actinomycete sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Evidence that high G+C contigs are bacterial. Contigs with a BLASTX match to the bacterial order Actinomycetales (at an expectation of 10-8 or less), plotted as a function of G+C content and contig length. Points are color-coded according to the taxonomy of the best GenBank match overall. There is a clean separation between contigs with lower G+C that are more similar, by percent identity and expectation of BLASTX sequence alignments, to arthropod sequences and contigs with higher G+C that are more similar to actinomycete sequences.
Mentions: We then examined G+C content of contigs (Figure 3), which suggested that Varroa nuclear DNA falls largely between 32-58% G+C content (40.9% G+C on average). Contigs with lower G+C content and higher coverage showed strong homology to mitochondrial and ribosomal DNA sequences previously reported for V. destructor, as would be expected. Contigs with higher G+C consistently showed higher sequence similarity to bacterial sequences than to arthropod sequences. For example, Figure 4 illustrates the distribution of contigs with BLASTX matches to the high G+C bacterial order Actinomycetales at an expectation of 10-8, plotted as a function of length and G+C content of contigs. Of these contigs, only those above approximately 58% G+C content were better matches (by sequence similarity and E-value) to Actinomycetales than to arthropods, or lacked an arthropod match entirely. Based on these considerations, we removed contigs outside the range of 32-58% G+C from the analyzed V. destructor assembly unless they contained a superior match to a eukaryotic sequence in GenBank at an expectation of 10-8. Additional filtering was performed as described in the Methods to specifically remove sequences from organisms that were considered potential contaminants a priori, such as known microbial pathogens of honey bees that are dispersed as spores.

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