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Sequencing and analysis of genes expressed in the cambial tissue of Quercus rubra using a normalized, large-insert cDNA library

WCU Author/Contributor (non-WCU co-authors, if there are any, appear on document)
Jesse Joseph Walsh (Creator)
Institution
Western Carolina University (WCU )
Web Site: http://www.wcu.edu/404.asp
Advisor
Wesley Bonds

Abstract: The logistical issues associated with completely sequencing a very large genome greatly limit the number organisms that can have such a project devoted to them. One of the methods developed to circumvent this impasse is the sequencing of expressed sequence tags (ESTs), that is, partial cDNAs. The technique is often used as an introduction to completely unsequenced genomes as well as a more detailed analysis of previously characterized genomes. In the case of poorly characterized genomes, EST sequencing provides a quick, efficient profile of the nucleotide sequences of messenger RNA. Furthermore, many plant ESTs have been quickly annotated via regions of sequence similarity comparisons with genes of model organisms such as the mustard, Arabidopsis thaliana Heynh, and the hardwood, Populus trichocarpa Torr. & A.Gray. This project focused on rapidly dividing cambial tissue from a Quercus rubra L. individual with a partially characterized ancestry. That individual was recovered from one of the few oak nurseries in the world, namely the Watauga Genetic Research Orchard near Elizabethton, TN. The cambial transcriptome provided 984 cDNA clones resulting in 870 unique sequences. After appropriate filtering the unique sequences were submitted for homology comparison against the gene databases of Arabidopsis, Populus, as well as the generalized UniProt database. Putative function was assigned to more than 90% of the unique sequences; however forty sequences have no significant homology to any known protein. The nucleotide sequences produced in this study will be submitted to the GenBank database where they will become the foundation for a Q. rubra sequence resource. Since the sequences were recovered from cambial tissue of spring wood, they will assist in better understanding wood formation within this species. Such studies should lead to increases in both the quality and quantity of this valuable hardwood found in western North Carolina.

Additional Information

Publication
Thesis
Language: English
Date: 2008
Keywords
DNA Sequencing, Expressed Sequence Tag, Quercus rubra
Subjects
Red oak -- Genetics
Red oak -- Genome mapping
Plant molecular biology