2012 Annual Report
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):
1) Continued genomic sequencing to 20x coverage with an ‘optimal’ mix of straight and end-pair 454 reads, followed by genome assembly;
2) Transcriptome surveys using 454 pyrosequencing, focused on: a) nymphal development, b) host finding (tarsal library), c) immune responses (gut with and without virus infection), and d) gut microbes;
3) SNP and protein polymorphism discovery using the ABI SOLiD platform on the mite transcriptome. Mites will be from the Midwestern, Southern, mid-Atlantic and Western U.S. as well as ‘outgroups’ from Australia and France. These data will be aligned with homologous sequence data from the genome reads (Maryland mite), and from the 454 transcriptome reads to give an abundance of SNPs; and
4) Development and testing of a canonical gene set and posting of emerging data via Beebase, NCBI, and other public databases.
The subcontract has focused on bioinformatic analyses for this project. A second genome assembly was built and is now available for the public. The results from these analyses are shared with mite and honey bee researchers and are actively being used to resolve weak points in Varroa mites as well as the availabilities of mites to carry viruses and other bee disease organisms. The subcontractee has posted genomic assembly and annotation data on their own servers and made this information accessible to a wide community.