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Title:   Author  item
                                            Geib, Scottitem
                                            Calla, Bernardaitem
                                            HALL, BRIAN - University Of Hawaiiitem
                                            HOU, SHAOBIN - University Of Hawaiiitem
                                            Manoukis, Nicholas
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 10/2/2014
                                    Publication  Date: 10/28/2014
                                    Citation: Geib, S.M., Calla Zalles, B., Hall, B., Hou, S., Manoukis, N. 2014. Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets. Biomed Central (BMC) Genomics. 15:942.Interpretive Summary: The oriental fruit fly is an important pest of fruits and vegetables in southeast Asia, the Pacific, and is a threat to mainland United States. Using high-throughput sequencing of the RNA of the species, the pattern of expression of the genes being expressed during development from egg to adult was characterized. In addition, these genes were compared to the genes present in the model insect species Drosophila melanogaster. Through this comparison, we are able to validate the results of our experiment, as well as compare and contrast gene expression between the species. This will serve as a foundation to functional genomics in this species and will help guide future research.
                                Technical Abstract: Background
The oriental fruit fly, Bactrocera dorsalis, is an important pest of fruit and vegetable crops throughout Asia, and is considered a high risk pest for establishment in the mainland United States. It is a member of the family Tephritidae, which are the most agriculturally important family of flies, and can be considered an out-group to well-studied members of the family Drosophilidae. Despite their importance as pests and their relatedness to Drosophila, little information is present on B. dorsalis transcripts and proteins. The objective of this paper is to comprehensively characterize the transcripts present throughout the life history of B. dorsalis and functionally annotate and analyse these transcripts relative to the presence, expression, and function of orthologous sequences present in Drosophila melanogaster.
  
Results
We present a detailed transcriptome assembly of B. dorsalis from egg through adult stages containing 20,666 transcripts across 10,799 unigene components. Utilizing data available through Flybase and the modENCODE project, we compared expression patterns of these transcripts to putative orthologs in D. melanogaster in terms of timing, abundance, and function. In addition, temporal expression patterns in B. dorsalis were characterized between stages, to establish the constitutive or stage-specific expression patterns of particular transcripts. A fully annotated transcriptome assembly is made available through NCBI, in addition to corresponding expression data.

Conclusions
Through characterizing the transcriptome of B. dorsalis through its life history and comparing the transcriptome of B. dorsalis to the model organism D. melanogaster, a database has been developed that can be used as the foundation to functional genomic research in Bactrocera flies and help identify orthologous genes between B. dorsalis and D. melanogaster. This data provides the foundation for future functional genomic research that will focus on improving our understanding of the physiology and biology of this species at the molecular level. This knowledge can also be applied towards developing improved methods for control, survey, and eradication of this important pest.


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