Bioinformatics analysis of transposons in S/MARs sequences

Abstract

The evolutionary relationship between five cereal grasses of the Gramineae were analyzed using a bioinformatics approach utilizing a DNA sequence known to be associated with scaffold/matrix attachment regions (SMARs) in wheat (Triticum aestivum), namely pSR14, to identify variants and transposable elements of the Stowaway family. This evaluation was executed using software and sequence data available through the National Center for Biotechnology Information (NCBI) housed at the National Library of Medicine. S/MARs and Stowaway elements have previously been established as important in understanding gene expression and the genomic changes within these related cereal grasses. The current number of sequence records, or LOC#s, identified from the BLASTn searches using the S/MARs pSR14 sequence was assessed. In addition, variants for each LOC# sequence was recorded. A frequency analysis was performed to compare the current number of sequence records among the five species. Limitations due to the nature of the bioinformatic data was noted and included in the analysis.