1a. Objectives (from AD-416)
The parasitic mite Varroa destructor is the central pest of domesticated and free-living honey bee, causing direct impacts on bee health as well as indirect effects caused by vectoring viruses and other bee disease agents. We propose to use emerging high-throughput sequencing techniques to sequence, assemble and annotate the genome of this mite, and use the resulting insights to improve honey bee health and crop pollination. We will increase project impacts through a cost-effective partnership across existing academic sequencing and informatics centers and by choosing appropriate sequencing techniques for specific questions. We will leverage this project by engaging ca. 40 academic and governmental researchers in a volunteer consortium, 22 of whom met along with nine industry leaders for an initial ‘Varroa Genome Workshop’ in January, 2009, at the American Beekeeping Federation Annual Convention, Reno Nevada.
1b. Approach (from AD-416)
We will continue genomic sequencing to 20x coverage with an ‘optimal’ mix of straight and end-pair 454 reads, followed by genome assembly. Transcriptome surveys will be carried out using 454 pyrosequencing, focused on 1) nymphal development, 2) host finding (tarsal library), 3) immune responses (gut with and without virus infection), and 4) gut microbes. SNPs and protein polymorphism will be discovered using the ABI SOLiD platform on the mite transcriptome. These data will be aligned with homologous sequence data from the genome reads and from the 454 transcriptome reads to give an abundance of SNPs. Development and testing of a canonical gene will be followed by Integration and posting of emerging data via Beebase, NCBI, and other public databases.
3. Progress Report
Genome sequencing is complete and gene annotation is underway. A complete Official Gene Set is expected to be complete by the end of September 2011. At that point, a whole genome microarray will be developed and tested to determine genes associated with host preference and virulence.