Progress 09/29/03 to 09/28/06
Outputs
Progress Report 4d Progress report. This report documents research conducted under a specific cooperative agreement between ARS and Baylor College of Medicine. Additional details of research can be found in the report for the in-house associated project 5430-43000-026-00D, Genomics and proteomics of stored-product insects for development of new biopesticides. In FY 2006 the entire genome sequence of Tribolium castaneum was examined to find each and every gene, using seven different gene-finding computer programs. A proposed set of 16,400 genes was tentatively identified, and this computer-generated set was selected as the starting point for verification by human experts. Organization, planning, and recruitment of personnel to accomplish the manual gene-checking effort, initiated at the International Tribolium Genetics meeting in Gottingen, Germany in 2005, has been completed, and the manual gene analysis has begun. The results of these analyses can be viewed with the
aid of the Tribolium genome browser at the Baylor College of Medicine, Human Genome Research Center, and will be ultimately be transferred to the BeetleBase database and website at Kansas State University. In addition, we have continued the process of determining the chromosomal location of each gene, and more than 80% of the Tribolium genome has now been mapped onto the chromosomes, approaching our goal of 90% by 2007. Identifying the functions of all these genes will have far-reaching impact on broad knowledge of insect genome evolution, physiological adaptations in pest and beneficial beetle species, and the identification of novel targets for pest control exploitation.
Impacts
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Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report documents research conducted under a specific cooperative agreement between ARS and Baylor College of Medicine. Additional details of research can be found in the report for the in-house associated project 5430-43000-026-00D, Genomics and proteomics of stored-product insects for development of new biopesticides. In FY 2005 the entire genome sequence of Tribolium castaneum was determined and assembled at the Baylor College of Medicine, Human Genome Research Center. We were able to map 75% of the entire genome onto the chromosomes by integrating the genetic and sequence maps. Refinements of the physical map will continue until both the genetic and physical maps can be fully integrated with the whole-genome sequence. We determined that additional mapping of the 40 largest unmapped sequence scaffolds will bring the genome mapping effort to 90% of completion. Efforts are now underway to accomplish this, and the task should be completed
in FY 2006. Organization, planning, and recruitment of personnel to accomplish the manual annotation effort was initiated at the International Tribolium Genetics meeting in Gottingen, Germany, and gene families were assigned to appropriate experts. The manual annotation will use the Ensembl gene prediction engine as a starting point, and will use the Apollo interface. The analysis of this sequence will have far-reaching impact on broad knowledge of insect genome evolution, physiological adaptations in pest and beneficial beetle species, and the identification of novel targets for pest control exploitation.
Impacts
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Progress 10/01/03 to 09/30/04
Outputs
4. What were the most significant accomplishments this past year? This report serves to document research conducted under a specific cooperative agreement between ARS and Baylor College of Medicine. Additional details of research can be found in the report for the parent project 5430-43000-023-00D, Functional genomics-based management of stored-product insect pests. In 2003, based on our white paper submitted to the National Human Genome Research Institute, the stored-product pest insect red flour beetle, Tribolium castaneum, was assigned a high priority rating for whole-genome sequencing, an accomplishment that had not previously been achieved for any agronomic pest species. We established the current SCA with the Baylor College of Medicine, Human Genome Research Center, to supplement the funds provided by the National Human Genome Research Institute for this project. We selected the GA2 strain of Tribolium for whole-genome sequencing, based on the rigorous
inbreeding regimen used to create it, and after rigorous confirmation of its near-homozygous inbred condition. This was accomplished by examination of more than 1000 SSCP loci, and by using Southern hybridization analysis to document loss of polymorphism in its normally hypervariable snapback DNA. We established a system of large-scale production of embryos from this highly inbred strain, and harvested 50 g of embryos for DNA extraction. The high-quality of sequence data obtained from this DNA was confirmed by analysis of the first 15,000 sequences from the genomic libraries. This accomplishment represents the joint efforts of CRIS 5430-43000-023, Kansas State University, and the Baylor College of Medicine Human Genome Sequencing Center. Sequence compilation and assembly will be done in 2004 and early 2005. The analysis of this sequence will have far-reaching impact on broad knowledge of insect genome evolution, physiological adaptations in pest and beneficial beetle species,
and the identification of novel targets for pest control exploitation.
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