|When:||Back to Calendar April 22, 2014 @ 10:00 am - 12:00 pm||Where:||7800 York Road #459
Towson University,Towson,MD 21252
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Student’s Name: Omar Darwish
Title of Thesis/Dissertation: Development of New Tools and Pipelines for Plant Bioinformatics Applications.
Department/Program: Computer and Information Sciences
Chair, Thesis/Dissertation Committee: Nadim Alkharouf
Committee Members: Darush Davani, Sungchul Hong, Kathy Wang
Plant Bioinformatics is a rapidly expanding field of study that involves applying computational methods to the analysis and management of large scale, high throughput, plant genomic experiments. We describe here the analysis and databases that were implemented for two very important plant crops, blueberry and strawberry. Blueberry is an economically and nutritionally important small fruit crop, native to North America. As with many crops, extreme low temperature can affect blueberry crop yield negatively and cause major losses to growers. For this reason, blueberry breeding programs have focused on developing improved cultivars with broader climatic adaptation. To help achieve this goal, the blueberry genomic database (BBGD454) was developed to provide the research community with valuable resources to identify genes that play an important role in flower bud and fruit development, cold acclimation and chilling accumulation in blueberry. Fragaria vesca, is a diploid strawberry species commonly known as the alpine or woodland strawberry. We developed the Strawberry Genomic Resources database (SGR) to provide a molecular description of floral organ and fruit development at the resolution of specific tissues and cell types. SGR is a web accessible database that contains sample description, sample statistics, gene annotation, and gene expression analysis. This information can be accessed publicly from a web-based interface at http://bioinformatics.towson.edu/strawberry. Taking advantage of the extensive transcriptomic data of fifty different tissue/stage samples of early stage F. vesca fruit development, we also re-annotated the F. vesca genome using the MAKER annotation pipeline. This re-annotation has significantly improved the accuracy of gene structure, introduced new gene models and will facilitate functional studies of individual strawberry genes.