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United States Department of Agriculture

Agricultural Research Service

Title: Charting Contig-Component Relationships Within the Triticeae : Exploiting the Genome (Chapter 8).

Authors
item Lazo, Gerard
item Lui, Nancy - UC DAVIS
item You, Frank - UC DAVIS
item Hummel, David - UC DAVIS
item Chao, Shiaoman - UC DAVIS
item Anderson, Olin

Submitted to: Genome Exploitation: Data Mining the Genome
Publication Type: Book / Chapter
Publication Acceptance Date: March 7, 2003
Publication Date: March 1, 2005
Citation: Lazo, G.R., Lui, N., You, F., Hummel, D., Chao, S., Anderson, O.D. 2005. Charting contig-component relationships within the triticeae: exploiting the genome (Chapter 8). Genome Exploitation: Data Mining the Genome. Springer Science, New York, NY. p. 109-120

Interpretive Summary: This is the first public demonstration of a gene-mining tool named "Contig Constellation Viewer" (CCV), and was presented as part of the 23rd Stadler Genetics Symposium. This tool was developed to assist the study of expressed sequence tags (ESTs) produced and sequenced for many grass family species, mainly wheat, barley and related species. With over 780,000 ESTs available for the Triticeae tribe (Poaceae Family), the tool was developed to allow comparison of sequence-derived attributes such as species, tissues, developmental stages, or conditional stresses. The tool provides a graphical interface to view the assembly of genes represented from the EST pool using different assembly programs. Presented are samples of patterns displayed by Triticeae assemblies and demonstration of how the CCV tool can be used for gene discovery research. Additional information may be obtained from a Triticeae resource page (http://wheat.pw.usda.gov/wEST) and the PWA Office of Technology Transfer.

Technical Abstract: There are now well over 780,000 expressed sequence tags (ESTs) from the Triticeae tribe (Poaceae Family) representing an abundance of cDNA library resources. These library resources from wheat, barley and related species can be categorized based on attributes such as species, tissues, developmental stages, conditional stresses. In tandem with the generation of this information there are several efforts underway to create consensus assemblies using different assembly algorithms. A gene-mining tool has been developed to interface with these assemblies and use relational databases to extract out information on relationships between the assembled contigs and the ESTs for these contigs. The CCV tool ("Contig Constellation Viewer"), allows an overview of the assembly method and provides an interface to query clusters viewed in an intuitive or directed manner. The CCV tool can be used to query how the contigs relate to the above mentioned attributes (species, tissues...), including other features such as mapped locations and metabolic pathways. Additional features include the ability to overlay results derived from other experiments as a potential gene-mining application. Presented are samples of display patterns exhibited by Triticeae contig assemblies and demonstration of how the CCV tool can be used for gene discovery research. Additional information may be obtained from a Triticeae resource page (http://wheat.pw.usda.gov/wEST).

Last Modified: 4/17/2014
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