Research
The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species
-
* Corresponding author: Eric J Richards ejr77@cornell.edu
1 Department of Biology, Washington University in St Louis, St Louis, MO, USA
2 Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
3 Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
Mobile DNA 2010, 1:10 doi:10.1186/1759-8753-1-10
Published: 1 March 2010Additional files
Additional file 1:
Divergence matrices of Arabidopsis thaliana Sadhu elements. Additional file 1 is a spreadsheet file containing divergence matrices of A. thaliana Sadhu elements, both within subfamilies and of consensus sequences across subfamilies. These matrices are based on ClustalX multiple sequence alignment.
Format: XLS Size: 42KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
Polymerase chain reaction (PCR) primers. Additional file 2 is a table listing PCR primers used in this study.
Format: DOC Size: 75KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 3:
DNA sequence information for Sadhu sequences greater than 350 base pairs (bp) in the Arabidopsis lyrata genome assembly. Additional file 4 provides DNA sequence information for Sadhu sequences greater than 350 bp in the Arabidopsis lyrata genome assembly. Target site duplications are indicated in purple and the conserved CAATCGTTSC motif is italicized and underlined. Non-Sadhu sequence inserted in the elements is in gray and italicized
Format: DOC Size: 53KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 4:
Partial Sadhu elements and flanking genomic sequences identified in Arabidopsis arenosa. Additional file 3 contains diagrams of partial Sadhu elements and flanking genomic sequences identified in A. arenosa. (a) Sadhu1; (b) Sadhu3; (c) Sadhu5; (d) Sadhu8. The scale is indicated. Internal polymerase chain reaction (PCR) sequences used specific primers based on the Arabidopsis thaliana sequence, while 5' and 3' sequences were obtained by thermal asymmetric interlaced (TAIL) PCR (see Table 4 for details). 5' Sadhu sequences are in blue, 3' Sadhu sequences are orange. Gray dotted arrows indicate the extent of Sadhu sequence homology. Features in flanking sequences are marked as green boxes. The inverted arrow in the annotation of the Aa5FP1 clone indicates the direction of transcription of the flanking gene-related sequence. Sadhu5 and Sadhu8 3' sequences feature poly(A) tracts at the Sadhu boundary, consistent with retrotransposition.
Format: PDF Size: 269KB Download file
This file can be viewed with: Adobe Acrobat Reader