Progress 10/01/12 to 09/30/13
Outputs
Progress Report 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 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. This project provides continued support for genome wide analysis of Bactrocera dorsalis 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". In the last year, research was focused at making initial releases of the oriental fruit fly genomic and transcriptomic databases. The oriental fruit fly RNA-Seq based transcriptome has been released as National Center for Biotechnology Information (NCBI) Bioproject PRJNA198716, including stage specfic expression analysis, structural and functional annotation. The draft assembly of the genome was released as NCBI bioproject PRJNA208397, including complete structural and functional annotation for the initial release of the genome. Throughout the year, communication between USDA, Agricultural Research Service (ARS), USDA Animal and PLant Health Inspection Service (APHIS), and collaborators providing samples for sequencing have been ongoing through email communication and teleconferencing to manage progress and funding availability. This includes the arrangement of samples being sent from International Atomic Energy Agency (IAEA) to USDA, ARS through the organization of USDA, APHIS.
Impacts
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Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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 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 5-10 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 researcher 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. This project provides continued support for genome wide analysis of Bactrocera dorsalis which contributes to Objective 5 of the in-house project. High throughput sequencing of approximately 48 populations of Bactrocera dorsalis has been completed. This includes samples from throughout South East Asia, as well as collections from the four major Hawaiian Islands through additional collecting that was completed this fiscal year. DNA extractions, library preparation, barcoding and sequencing was completed. Initial analysis of the data reveals about 20,000 loci that appear to be informative to identify populations of B. dorsalis, but more detailed analysis still needs to be completed. All of the data is loaded on a mysql database to facilitate data sharing and interactions. In addition, annotation and analysis of the B. dorsalis genome is complete for dissemination. Throughout the year, communication between USDA-ARS, USDA-APHIS, and collaborators providing samples for sequencing have been ongoing through email communication and teleconferencing to manage progress and funding availability. This includes the arrangement of samples being sent from IAEA to USDA-ARS through the organization of USDA-APHIS. In addition, this project was discussed in detail at a workshop held at USDA-APHIS- CPHST, Edinburg, TX in January 2012.
Impacts
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Publications
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