Open Access Highly Accessed Research article

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

R Scott Cornman1, Michael C Schatz2, J Spencer Johnston3, Yan-Ping Chen1, Jeff Pettis1, Greg Hunt1, Lanie Bourgeois5, Chris Elsik6, Denis Anderson7, Christina M Grozinger8 and Jay D Evans14*

Author Affiliations

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

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BMC Genomics 2010, 11:602  doi:10.1186/1471-2164-11-602

Published: 25 October 2010

Additional files

Additional file 1:

Annotation statistics for filtered high G+C contigs. Annotation statistics derived from the BLAST2GO annotation tool [34]. A. Distribution of BLASTX hits (E ≤ 10-10) by organism. Note that the "Others" category is typically the most abundant in this type of analysis because of the wide taxonomic distributions of many conserved proteins. B. Distribution of BLASTX hits by sequence similarity score. C. Distribution of BLASTX hits by expectation.

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Additional file 2:

Contigs identified as deriving from a novel virus of the Baculoviridae. Fasta-formatted contigs were classified as described in text. Also included are the methionine-initiated ORFs of 90 codons or more that are referenced in Table 3.

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Additional file 3:

BLAST-annotated Varroa contigs. Spreadsheet of Varroa destructor genomic contigs with significant similarity to the GenBank nr database by BLAST search.

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Additional file 4:

ORFs with Pfam domains. Spreadsheet of significant Pfam domains within ORFs having BLASTP-detected similarity to GenBank sequences.

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Additional file 5:

ORFs referenced in Additional file 3and Additonal file 4. Fasta-formatted ORFs from V. destructor contigs that had significant sequence similarity to database sequences.

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Additional file 6:

Comparison of ORF codon usage for contigs assigned as either Varroa destructor or bacterial in origin. Scatterplot comparing G+C content and codon usage of ORFs from contigs assigned as either Varroa destructor or bacterial. The X-axis value is third position G+C and the Y-axis value is the codon usage statistic B [62], which as used here is a measure of the difference in codon usage between each subgroup of ORFs relative to the whole. The possible range of values for B is 0 to 2, with larger values corresponding to greater divergence in codon frequencies. A. Residual contigs after filtering, which are assumed to all derive from V. destructor. B. Contigs filtered because they have a higher BLAST score to bacterial sequences than to eukaryotic sequences. The two groups of contigs have distinct patterns of codon usage and nucleotide composition.

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Additional file 7:

Microsatellite loci used in Varroa destructor polymorphism survey. Table lists contig containing the microsatellite locus, forward and reverse primer sequences, expected product size based on the reference contig, and the 5' start coordinate on the contig for the forward primer.

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