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United States Department of Agriculture

Agricultural Research Service

Title: Towards a genome sequence for reniform nematode (Rotylenchulus reniformis))

item Bartlett, Benjamin
item Shan, Xueyan
item Wubben, Martin
item Jenkins, Johnie
item Peterson, Daniel

Submitted to: Meeting Abstract
Publication Type: Abstract only
Publication Acceptance Date: 4/1/2008
Publication Date: 4/18/2008
Citation: Bartlett, B.D., Shan, X., Wubben, M., Jenkins, J.N., Peterson, D.G. 2008. Towards a genome sequence for reniform nematode (Rotylenchulus reniformis) [abstract]. Proceedings Tougaloo College-Mississippi College 5th Undergraduate Research Symposium, April 18, 2008, Tougaloo, MS.

Interpretive Summary:

Technical Abstract: Reniform nematode (Rotylenchulus reniformis) currently accounts for $130M in annual losses to the U.S. cotton industry and has supplanted root-knot nematode as the major nematode pest of cotton in Mississippi, Louisiana, and Alabama. Moreover, in other cotton-producing states the range and influence of reniform nematode is growing rapidly. There is no natural resistance to reniform nematode in commercial cotton lines. As a means to better understand reniform nematode and limit the damage it causes, we have initiated a project to sequence the Rotylenchulus reniformis genome. The R. reniformis genome sequence will be used to develop strategies that selectively disrupt key metabolic/developmental pathways and consequently may afford a highly targeted means of controlling this pest. To date we have generated a bacterial artificial chromosome (BAC) library for R. reniformis. The library contains 32 genome equivalents of reniform nematode DNA. Each of the 21,504 clones is archived in its own well of a microtiter plate. The mean insert size of the clones is 75 kb. Our plan is to fragment each BAC and then add a synthetic “bar code” (i.e., an oligonucleotide containing a primer sequence and a unique identification region) onto the 5’ ends of fragments. Groups of 96 differentially bar-coded BACs will be pooled and sequenced using an ultra-throughput sequencer (e.g., a 454 FLX and/or an Illumina DNA Analyzer). After sequencing, an automated data analysis pipeline will place reads into BAC-specific groups based upon their bar codes. Each BAC will then be assembled in silico, and a complete (or nearly complete) consensus sequence will be produced. A physical map of the R. reniformis genome will then be constructed based upon actual BAC sequence overlap. Once completed, we will use a comparative genomics approach to identify genetic pathways that can be selectively targeted in reniform nematode control.

Last Modified: 8/24/2016
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