Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): The parasitic mite Varroa destructor is the central pest of domesticated and free-living honey bees, causing direct impacts on bee health as well as indirect effects caused by vectoring viruses and other bee disease agents. Genomic information for this pest can be used to develop gene- based control strategies, determine weak points for conventional (chemical) controls, identify targets for biological control, and show how mites find honey bee hosts and reproduce in resistant and susceptible bee lineages. We will use emerging high-throughput sequencing techniques to sequence, assemble and annotate (describe key traits of) the genome of this mite. Sequencing will be completed in the first year of the project and released publically into genomic databases. Gene expression work aimed at discovering mite weaknesses will be completed in the second year and targets for mite control will be identified throughout the project. We will increase project impacts through a cost-effective partnership across existing 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. The resulting insights will be used to improve honey bee health and crop pollination. Approach (from AD-416): We will carry out genomic sequencing exceeding 60X coverage of the 565 million base-pair genome of Varroa destructor with an �optimal� mix of straight and end-pair SOLEXA genomic sequencing reads, followed by genome assembly and pipeline annotation with resources provided by the US National Institutes of Health, NCBI. Specifically, we will carry out three SOLEXA flow cell runs with straight (72 bp) reads generated from Varroa genomic DNA templates and one SOLEXA endpair run (72 bp) generated from the same source material. Transcriptome surveys will be carried out using ROCHE Titanium pyrosequencing, focused on 1) nymphal development, 2) host finding (tarsal library), 3) immune responses (gut with and without virus infection), and 4) gut microbes. Single-nucleotide polymorphisms (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 set will be followed by integration and posting of emerging data via Beebase, NCBI, and other public databases. In the past year Bee Research Laboratory (BRL) completed the genomic assembly of the Varroa genome, and directed the sequencing of RNA from nine distinct tissues and life stages. The current effort is focused on producing a gene list for Varroa and identifying proteins that are suitable targets for RNA interference and the development of safer chemical controls. Two ARS-led papers between BRL and researchers in Gainesville, Florida used genomic insights to describe the process of mite reproduction.
Impacts
(N/A)
Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): The parasitic mite Varroa destructor is the central pest of domesticated and free-living honey bees, causing direct impacts on bee health as well as indirect effects caused by vectoring viruses and other bee disease agents. Genomic information for this pest can be used to develop gene- based control strategies, determine weak points for conventional (chemical) controls, identify targets for biological control, and show how mites find honey bee hosts and reproduce in resistant and susceptible bee lineages. We will use emerging high-throughput sequencing techniques to sequence, assemble and annotate (describe key traits of) the genome of this mite. Sequencing will be completed in the first year of the project and released publically into genomic databases. Gene expression work aimed at discovering mite weaknesses will be completed in the second year and targets for mite control will be identified throughout the project. We will increase project impacts through a cost-effective partnership across existing 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. The resulting insights will be used to improve honey bee health and crop pollination. Approach (from AD-416): We will carry out genomic sequencing exceeding 60X coverage of the 565 million base-pair genome of Varroa destructor with an �optimal� mix of straight and end-pair SOLEXA genomic sequencing reads, followed by genome assembly and pipeline annotation with resources provided by the US National Institutes of Health, NCBI. Specifically, we will carry out three SOLEXA flow cell runs with straight (72 bp) reads generated from Varroa genomic DNA templates and one SOLEXA endpair run (72 bp) generated from the same source material. Transcriptome surveys will be carried out using ROCHE Titanium pyrosequencing, focused on 1) nymphal development, 2) host finding (tarsal library), 3) immune responses (gut with and without virus infection), and 4) gut microbes. Single-nucleotide polymorphisms (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 set will be followed by integration and posting of emerging data via Beebase, NCBI, and other public databases. With nearly 100 million DNA sequences, the Bee Research Lab (BRL) has built a second-generation genomic assembly for Varroa destructor, and has started to annotate that assembly with insights from RNA sequencing. A group of 30 scientists has formed for annotation and writing and BRL is leading this effort through shared �cloud� Web sites and dialogue to maximize the agricultural impact of identifying genes for this important pest. Four institutions are using the genomic data to develop novel (RNA interference) techniques for controlling varroa mites in beehives.
Impacts
(N/A)
Publications
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) The parasitic mite Varroa destructor is the central pest of domesticated and free-living honey bees, causing direct impacts on bee health as well as indirect effects caused by vectoring viruses and other bee disease agents. Genomic information for this pest can be used to develop gene- based control strategies, determine weak points for conventional (chemical) controls, identify targets for biological control, and show how mites find honey bee hosts and reproduce in resistant and susceptible bee lineages. We will use emerging high-throughput sequencing techniques to sequence, assemble and annotate (describe key traits of) the genome of this mite. Sequencing will be completed in the first year of the project and released publically into genomic databases. Gene expression work aimed at discovering mite weaknesses will be completed in the second year and targets for mite control will be identified throughout the project. We will increase project impacts through a cost-effective partnership across existing 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. The resulting insights will be used to improve honey bee health and crop pollination. Approach (from AD-416) We will carry out genomic sequencing exceeding 60X coverage of the 565 million base-pair genome of Varroa destructor with an �optimal� mix of straight and end-pair SOLEXA genomic sequencing reads, followed by genome assembly and pipeline annotation with resources provided by the US National Institutes of Health, NCBI. Specifically, we will carry out three SOLEXA flow cell runs with straight (72 bp) reads generated from Varroa genomic DNA templates and one SOLEXA endpair run (72 bp) generated from the same source material. Transcriptome surveys will be carried out using ROCHE Titanium pyrosequencing, focused on 1) nymphal development, 2) host finding (tarsal library), 3) immune responses (gut with and without virus infection), and 4) gut microbes. Single-nucleotide polymorphisms (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 set will be followed by integration and posting of emerging data via Beebase, NCBI, and other public databases. This project contributes to a genome project for Varroa mites, a central pest of honey bees worldwide, and a component of the parent project objective of managing pests to improve colony health. A total of 4 million DNA sequences for this mite have been generated and deposited publically at the US-NIH Genbank, and a descriptive paper of the genome has been accepted for publication. Two Invention disclosures have been filed describing potential biocontrol microbes for these mites. One peer- reviewed publication describing the draft genome sequencing of the Varroa mite has been published, and a complete inventory of current resources submitted to Genbank. Proteins identified in this ARS project are being used by several laboratories to improve upon Varroa controls, including novel RNA interference controls. This is an international collaborative project.
Impacts
(N/A)
Publications
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) The parasitic mite Varroa destructor is the central pest of domesticated and free-living honey bees, causing direct impacts on bee health as well as indirect effects caused by vectoring viruses and other bee disease agents. Genomic information for this pest can be used to develop gene- based control strategies, determine weak points for conventional (chemical) controls, identify targets for biological control, and show how mites find honey bee hosts and reproduce in resistant and susceptible bee lineages. We will use emerging high-throughput sequencing techniques to sequence, assemble and annotate (describe key traits of) the genome of this mite. Sequencing will be completed in the first year of the project and released publically into genomic databases. Gene expression work aimed at discovering mite weaknesses will be completed in the second year and targets for mite control will be identified throughout the project. We will increase project impacts through a cost-effective partnership across existing 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. The resulting insights will be used to improve honey bee health and crop pollination. Approach (from AD-416) We will carry out genomic sequencing exceeding 60X coverage of the 565 million base-pair genome of Varroa destructor with an �optimal� mix of straight and end-pair SOLEXA genomic sequencing reads, followed by genome assembly and pipeline annotation with resources provided by the US National Institutes of Health, NCBI. Specifically, we will carry out three SOLEXA flow cell runs with straight (72 bp) reads generated from Varroa genomic DNA templates and one SOLEXA endpair run (72 bp) generated from the same source material. Transcriptome surveys will be carried out using ROCHE Titanium pyrosequencing, focused on 1) nymphal development, 2) host finding (tarsal library), 3) immune responses (gut with and without virus infection), and 4) gut microbes. Single-nucleotide polymorphisms (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 set will be followed by integration and posting of emerging data via Beebase, NCBI, and other public databases. This project report describes a newly funded NIFA grant to build a genome project for Varroa mites, a central pest of honey bees worldwide. A total of 4 million DNA sequences for this mite have been generated and deposited publicly at the US-NIH Genbank, and a descriptive paper of the genome has been accepted for publication. Two Invention disclosures have been filed describing potential biocontrol microbes for these mites, and the genome sequences have enabled several laboratories to study RNA interference as a novel control for mites.
Impacts
(N/A)
Publications
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