Page Banner

United States Department of Agriculture

Agricultural Research Service

Title: The Whitefly Bemisia Tabaci Est Database: Bioformatics and Data Management

Authors
item Brown, J. - UNIVERSITY OF ARIZONA
item Czosnek, H. - HEBREW UNIV. OF JERUS
item Merchant, N. - UNIVERSITY OF ARIZONA
item McKenzie, Cindy
item Shatters, Robert

Submitted to: European Whitefly Symposium Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: May 11, 2004
Publication Date: September 12, 2004
Citation: Brown, J.K., Czosnek, H., Merchant, N., Mckenzie, C.L., Shatters, R.G. 2004. The whitefly bemisia tabaci est database: bioformatics and data management. European Whitefly Symposium Proceedings.

Technical Abstract: This B. tabaci expressed sequence tag (EST) library and associated cDNA database is under development to analyze how begomoviruses influence the whitefly transcript profile including the begomovirus circulative transmission, and virus-induced changes in whitefly immune defense gene expression and measurable fecundity. The cDNA libraries were constructed by pooling populations of B biotype from Israel, Florida, and Arizona selected before and after they ingest a monopartite (Tomato yellow leaf curl virus, TYLCV) or bipartite begomovirus (Tomato mottle virus, ToMoV). As an economical approach to identifying fewer redundant clones, 200,000 arrayed cDNA clones were screened for homology to 500 previously sequenced whitefly cDNAs. The sequence will be determined for those not hybridizing with the 500 clones. A database is under construction that will house whitefly ESTs, which will be subjected to BLAST analyses against sequences available in public databases, and other relevant bioinformatics evaluations. Raw cDNA sequences are processed through a pipeline that utilizes Phred as the base-calling algorithm, FAKTORY for editing and contig construction, BLAST analysis, and SCOOT for organizing cDNA sequences and output BLAST results, together with other relevant software. A project website, WHITEFLY-BASE, is under construction, which will permit access to B. tabaci cDNA sequences. The results of BLAST analyses will be organized at the site such that users can compare their own project sequences to those obtained here. This project combines expertise in B. tabaci biology, plant-virus-vector relationship, genomics and bioinformatics, and is presented with the knowledge that elucidating molecular mechanisms underlying the biology of B. tabaci is a requisite to devising new strategies to curb the disastrous effects of this insect pest and virus vector in crop species, worldwide.

Last Modified: 8/27/2014
Footer Content Back to Top of Page