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Open Access Research article

Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes

Yujun Han1, Shanshan Qin1 and Susan R Wessler12*

Author Affiliations

1 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA

2 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

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BMC Genomics 2013, 14:71  doi:10.1186/1471-2164-14-71

Published: 31 January 2013

Additional files

Additional file 1:

Summary of Class 2 transposable elements from five superfamilies in four sequenced grass genomes.

Format: XLSX Size: 15KB Download file

Open Data

Additional file 2:

The double-ended copy number and length of the consensus nTEs of Tc1/mariner, PIF/Harbinger, hATand Mutatorin Brachypodium, rice, sorghum and maize. The y-axis is in log10 scale.

Format: TIFF Size: 8.4MB Download file

Open Data

Additional file 3:

Total length of nTEs from each superfamily genome-wide, intergenic and in four genic compartments.

Format: XLSX Size: 20KB Download file

Open Data

Additional file 4:

Distribution of nTE sequence frequency within introns of Brachypodium (A), rice (B), sorghum (C) and maize (D). The left and right starting points represent the 5 and 3 borders of introns, respectively. Colors of superfamilies are the same as in Figure  1.

Format: TIFF Size: 16.5MB Download file

Open Data

Additional file 5:

Comparison of the expression of genes associated with different class 2 TE superfamily members vs. genes without class 2 TEs (control) (using microarray data).

Format: XLSX Size: 13KB Download file

Open Data

Additional file 6:

Comparison of the expression of genes associated with different class 2 TE superfamily members vs. genes without class 2 TEs (control) (using RNA-seq data).

Format: XLSX Size: 10KB Download file

Open Data