Genome Wide Sequencing and Analysis of Bactrocera Species Complex
Tropical Crop and Commodity Protection Research
2013 Annual Report
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 a PBARC research entomologist 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. Formerly 5320-22430-023-04R; 6/2011.
The goal of this research is to perform genome-wide analysis of several members of the oriental fruit fly species complex which contributes to objective 5 of the in-house project, "Develop basic understanding of the oriental fruit fly genome, annotation of functional proteins that regulate development, metabolism, sensory reception and sex determination".
From high throughput sequencing of approximately 48 populations of Bactrocera dorsalis performed in the previous year, including samples from throughout South East Asia, as well as collections from the four major Hawaiian Islands, single nucleotide polymorphism (SNP) markers that can be used to discriminate Hawaiian populations from flies of Southeast Asian orgin were found. From this collection of SNPs (105 high quality SNPs), a subset are being used to create a SNP based diagnostic tool for USDA Animal and Plant Health Inspection Service (APHIS) to use to determine source of flies. In addition, there are many more markers that appear to be informative to identify populations of B. dorsalis within Southeast Asia, but have not been utilized in a SNP assay.