1a. Objectives (from AD-416)
The objective of this research is to perform genome-wide analysis of several members of the Oriental fruit fly species complex with focus on: • Identification of gene regions for use in species-level diagnosis based on these genomes • Identification of gene regions that demonstrate poor performance for diagnostics (and should not be included in screening studies) • Identification of population-level markers for pathway analysis and population structure studies (these markers should be useful across species boundaries and provide markers for various bactrocera and fruit fly species) • Comparative phylogenomics analysis of the included species to direct future studies and test species boundaries
1b. Approach (from AD-416)
Comparative genomic analysis within the dorsalis complex will be performed by using pyrosequencing technology to generate several “shallow” (low coverage) genomes from Bactrocera species and analyze them using bioinformatic tools. Using five-ten fruit fly specimens representing Bactrocera species in the dorsalis complex our team will generate genomic databases for each specimen using a 454 pyrosequencer operated at the University of Hawaii. This genomic work will be designed and supervised by Dr. Scott Geib who is currently in charge of annotating the completed Bactrocera dorsalis genome. The species included for genomic analysis will be selected based on similarity to B. dorsalis, economic significance, and value to SIT programs. The data generated using 454 technology will be edited, annotated and analyzed by CPHST and ARS staff. Documents Reimbursable with USDA-APHIS-CPHST. Log 42092
3. Progress Report
Initial plans were discussed between APHIS-CPHST and PBARC on the specific approaches to use for genome wide sequencing of members of the Bactrocera dorsalis complex. A reduced representation restriction site associated DNA marker sequencing (RAD sequencing) approach is being taken and methods for sample prep are currently being developed at PBARC. Samples from multiple locations in East Asia were selected for analysis (B. dorsalis, B. papayae, B. phillipinensis, and B. carambolae) and are planned to be sent to PBARC for analysis. Access of up to 264 fly samples within this complex is being made available to the project by Karen Armstrong at Lincoln University, Canterbury, New Zealand. Funds were transferred to University of Hawaii Manoa Sequencing Facility to provide sequencing services for this project on a 454 pyrosequencer and Illumnia GAIIx over the next year.