Fly Base - Related Research

Related Research

The following is only two of many examples of research that is related to or uses FlyBase: 1. The first is a study of expressed genes from alate Toxoptera citricida, more commonly known as the brown citrus aphid. The brown citrus aphid, is considered the primary vector of citrus tristeza virus, a severe pathogen which causes losses to citrus industries worldwide. The winged form of this aphid can fly long distances with the wind, enabling them to spread the citrus tristeza virus in citrus growing regions. To better understand the biology of the brown citrus aphid and the emergence of genes expressed during wing development, researchers undertook a large-scale 5′ end sequencing project of cDNA clones from winged aphids. Similar large-scale expressed sequence tag (EST) sequencing projects from other insects have provided a vehicle for answering biological questions relating to development and physiology. Although there is a growing database in GenBank of ESTs from insects, most are from Drosophila melanogaster, with relatively few specifically derived from aphids.The researchers were able to provide a large data set of ESTs from the alate (winged) brown citrus aphid and have begun to analyze this valuable resource. They were able to do this with the help of information on Drosophila melanogaster in FlyBase. Putative sequence identity was determined using BLAST searches. Sequence matches with E-value scores ≤ −10 were considered significant and were categorized according to the Gene Ontology (GO) classification system based on annotation of the 5 ‘best hit’ matches in BLASTX searches. All D. melanogaster matches were cataloged using FlyBase. Nearly all of these ‘best hit’ matches were characterized with respect to the functionally annotated genes in D. melanogaster using FlyBase. Genetic information is crucial to advancing the understanding of aphid biology, and will play a major role in the development of future non-chemical, gene-based control strategies against these insect pests. 2.Enhancing Drosophila Gene Ontology Annotation: What gene products do and where they do it are important questions for biologists. The Gene Ontology project was established 13 years ago in order to summarize this data consistently across different databases by using a common set of defined vocabulary terms. They also encode relationships between terms. The Gene Ontology Project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project also provides gene product annotation data from GO consortium members. />.) This is where FlyBase comes in. FlyBase was one of the three founding members of the Gene Ontology Consortium. GO annotation comprises at least three components: a GO term that describes molecular function, biological role or subcellular location; an ‘evidence code’ that describes the type of analysis used to support the GO term; and an attribution to a specific reference. GO annotation is useful for both small-scale and large-scale analyses. It can provide a first indication of the nature of a gene product and, in conjunction with evidence codes, point directly to papers with pertinent experimental data. The current priorities for annotation are: homologs of human disease genes, genes that are highly conserved across species, genes involved in biochemical/signaling pathways, and topical genes shown to be of significant interest in recent publications. FlyBase has been contributing GO annotations to the project since it started in August 2006. GO annotations appear on the Gene Report page in FlyBase. GO data are searchable in FlyBase using both TermLink and QueryBuilder. The GO is dynamic and can change on a daily basis, for example the addition of new terms. To keep up, FlyBase loads a new version of the GO every one or two releases of FlyBase. The GO annotation set is submitted to the GOC at the same time as a new version of FlyBase is released.