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Article
Gene expression patterns are correlated with genomic and genic structure in soybean
Genome
  • Jenna L. Woody, Iowa State University
  • Andrew J. Severin, Iowa State University
  • Yung-Tsi Bolon, United States Department of Agriculture
  • Bindu Joseph, Iowa State University
  • Brian W. Diers, University of Illinois at Urbana-Champaign
  • Andrew D. Farmer, National Center for Genome Resources
  • Nathan Weeks, United States Department of Agriculture
  • Gary J. Muehlbauer, University of Minnesota
  • Rex T. Nelson, United States Department of Agriculture
  • David Grant, United States Department of Agriculture
  • James E. Specht, University of Nebraska–Lincoln
  • Michelle A. Graham, United States Department of Agriculture
  • Steven B. Cannon, United States Department of Agriculture
  • Gregory D. May, National Center for Genome Resources
  • Carroll P. Vance, University of Minnesota
  • Randy C. Shoemaker, United States Department of Agriculture
Document Type
Article
Publication Version
Published Version
Publication Date
1-1-2011
DOI
10.1139/G10-090
Abstract
Studies have indicated that exon and intron size and intergenic distance are correlated with gene expression levels and expression breadth. Previous reports on these correlations in plants and animals have been conflicting. In this study, next-generation sequence data, which has been shown to be more sensitive than previous expression profiling technologies, were generated and analyzed from 14 tissues. Our results revealed a novel dichotomy. At the low expression level, an increase in expression breadth correlated with an increase in transcript size because of an increase in the number of exons and introns. No significant changes in intron or exon sizes were noted. Conversely, genes expressed at the intermediate to high expression levels displayed a decrease in transcript size as their expression breadth increased. This was due to smaller exons, with no significant change in the number of exons. Taking advantage of the known gene space of soybean, we evaluated the positioning of genes and found significant clustering of similarly expressed genes. Identifying the correlations between the physical parameters of individual genes could lead to uncovering the role of regulation owing to nucleotide composition, which might have potential impacts in discerning the role of the noncoding regions.
Comments

This article is from Genome, 2011, 54(1): 10-18, 10.1139/G10-090.

Rights
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.
Language
en
File Format
application/pdf
Citation Information
Jenna L. Woody, Andrew J. Severin, Yung-Tsi Bolon, Bindu Joseph, et al.. "Gene expression patterns are correlated with genomic and genic structure in soybean" Genome Vol. 54 Iss. 1 (2011) p. 10 - 18
Available at: http://works.bepress.com/nathan-weeks/1/