2013 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, coordinated by USDA-ARS Beltsville colleagues, and colleagues at the University of Maryland for informatics help.
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 gathered by (Midwestern US), (South), mid-Atlantic and Pacific west) 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.
4) Development and testing of a canonical gene set. All in consortium involved, with help from (NCBI).
5) Integration and posting of emerging data via Beebase, NCBI, and other public databases with assistance from Purdue University, as a bridge to tick genomics and VectorBase).
The subcontract is being used to explore differences across mites in their impacts on bees and in their ability to survive chemical exposure. The subcontractee continues to work on genome variants that are involved with mite virulence.