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United States Department of Agriculture

Agricultural Research Service

Title: Bioinformatics Analysis of Predicted S/Mars and Associated Stowaway Transposon Locations in the Gramineae

item Delongchamp, Sarah
item Blakey, Ann
item Christoffers, Michael
item Gustafson, J

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/15/2007
Publication Date: 1/15/2008
Citation: Delongchamp, S.R., Blakey, A.C., Christoffers, M., Gustafson, J.P. 2008. Bioinformatics Analysis of Predicted S/Mars and Associated Stowaway Transposon Locations in the Gramineae [abstract]. Plant and Animal Genome Conference, January 2008, San Diego, California. Paper No. P267.

Interpretive Summary:

Technical Abstract: The wheat genome contains an enormous diversity in organization and variation in types of DNA sequences, which play important roles in the organization and functioning of the wheat genomes. Scaffold/Matrix Attachment Regions (S/MARs) are sequences of DNA that anchor chromatin to the nuclear matrix and function in gene expression, chromatin organization, and conformation. Current identification tools rely on a small population of known S/MARs for search criterion. Two wheat S/MARs were used to identify homologous sequences, particularly within the true Grasses, or Gramineae. The evidence suggests that S/MARs are prolific in Gramineae species, specifically in the related subspecies of the Triticeae. Also, Stowaway-like sequences found in association with predicted S/MARs in the Gramineae were found to be the product of non-random duplication though their association with S/MARs. This study presents the bioinformatics predictions of S/MARs across various genomes using NCBI BLAST, and provides an opportunity to identify novel putative S/MARs in related genomes for further characterization of associated genic regions. In addition, an analysis of Stowaway-like sequences associated with predicted S/MARs within Gramineae species are presented. The results suggested that variation in types of DNA sequences impact the structure of genes and chromosomes among the various grass species.

Last Modified: 06/28/2017
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