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Open Access Research article

The complete Ac/Ds transposon family of maize

Chunguang Du1*, Andrew Hoffman1, Limei He2, Jason Caronna1 and Hugo K Dooner23*

Author Affiliations

1 Dept. of Biology & Molecular Biology, Montclair State University, Montclair, NJ 07043, USA

2 Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA

3 Dept. of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA

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BMC Genomics 2011, 12:588  doi:10.1186/1471-2164-12-588

Published: 1 December 2011

Additional files

Additional file 1:

Supplemental tables. Table S1. PCR primers used to assay Ds and Ds-l somatic excisions. Table S2. Description of Ds1 elements. Table S3. Description of Ds2 elements. Table S4. Description of Ds3 elements. Table S5. Description of Ds4 elements.

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Additional file 2:

Figure S1. - Phylogenetic tree of 456 Ds-l4 elements. All Ds-l4 elements other than the 30 containing insertions of known transposons, were aligned by the high-speed multiple sequence alignment program MAFFT (Multiple Alignment using Fast Fourier Transform) http://www.ebi.ac.uk/Tools/msa/mafft/ webcite. The phylogenetic tree with the shortest branch lengths was built by Jalview software using the neighbor joining algorithm. Three major clusters of filler sequences are identified. There are 57 elements in cluster 1 which is the top part of the phylogenetic tree and 60 elements in cluster 3, the bottom part of the tree. These clusters are relatively more divergent than cluster 2, which is the largest one with 339 elements in the middle of the phylogenetic tree.

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Additional file 3:

Figure S2. Distribution of Ds elements in each of the 10 B73 pseudomolecules. The X axis shows the length of each chromosome in megabases (Mb) and the y axis shows the number of Ds insertions in each 5-Mb bin. Approximate centromere positions are indicated with a black circle.

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