Open Access Research article

Horizontal transfer of OC1 transposons in the Tasmanian devil

Clement Gilbert1, Paul Waters23, Cedric Feschotte4 and Sarah Schaack5*

Author Affiliations

1 Université de Poitiers, UMR CNRS 7267, Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France

2 Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australia

3 School of Biotechnology & Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia

4 Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA

5 Department of Biology, Reed College, Portland, OR, USA

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BMC Genomics 2013, 14:134  doi:10.1186/1471-2164-14-134

Published: 27 February 2013

Additional files

Additional file 1:

A FASTA file containing the consensus sequence of OC1_Das autonomous (OC1_Das-Auto) and non-autonomous elements (OC1_Das-NA). The transposase gene lies between position 565 and 2370 within OC1_Das-Auto.

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Additional file 2: Figure S1:

Phylogenetic relationships of individual copies of OC1_Das. Thirty full (or nearly full) length autonomous elements were randomly selected and a multiple alignment was built using ClustalW in BioEdit 5.8 [28]. The name of the sequences corresponds to the GenBank accession number of the contig from which they were extracted, followed by the position within each contig of the OC1_Das sequence that was used in the analysis. The tree was constructed using the neighbor-joining method in MEGA 4.0 ([29]; maximum-likelihood composite model; 1,000 bootstrap pseudoreplicates). Bootstrap values are not shown because they are all lower than 50.

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Additional file 3: Figure S2:

Distribution of percent divergence between each copy of OC1_Das and the consensus element.

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Additional file 4:

A FASTA file containing the OC1_Das-Auto and OC1_Das-NA consensus sequences aligned with two copies of OC1_Das-NA sequenced from the Tasmanian devil Sarcophilus harrisii (OC1_Das_NA-Sh1-2) and four copies of OC1_Das-NA sequenced from the dunnart, Sminthopsis crassicaudata (OC1_Das_NA-Sc1-4). While positions 1–58 and 104–192 of OC1_Das_NA are homologous to the 5′ and 3′ region of OC1_Das-Auto, respectively, the internal region of OC1_Das_NA (positions 59–103) has an unknown origin. The internal region of OC1_Das_NA-Sc is also from an unknown origin and it is different from that of OC1_Das_NA-Sh. The sequence of the primers used to amplify OC1_Das_NA (melting temperature = 55 degrees) in both species is also included in the alignment (OC1_Das_NA_F/R-55).

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Additional file 5:

A FASTA file containing a copy of OC1_Das_NA extracted from the Tasmanian devil genome (contig GL962536) with its 5′ and 3′ flanking regions aligned with their homologous loci in Macropus eugenii (ABQO010294817), Monodelphis domestica (AAFR03026483) and Sminthopsis crassicaudata (empty site 1 sequenced in this study using primers F/R2536 with a PCR melting temperature of 53 degrees). OC1_Das_NA is present in the Tasmanian devil (position 212–403 of contig GL962536) and is absent from the three other species.

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Additional file 6:

A FASTA file containing a copy of OC1_Das_NA extracted from the Tasmanian devil genome (contig GL972772) with its 5′ and 3′ flanking regions aligned with their homologous loci in Macropus eugenii (ABQO010316396), Monodelphis domestica (AAFR03014268) and Sminthopsis crassicaudata (empty site 2 sequenced in this study using primers F/R2772 with a PCR melting temperature of 55 degrees). OC1_Das_NA is present in the Tasmanian devil (position 494–684 of contig GL972772) and is absent from the three other species.

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Additional file 7:

A FASTA file containing a copy of OC1_Das_NA extracted from the Tasmanian devil genome (contig GL964687) with its 5′ and 3′ flanking regions aligned with their homologous loci in Macropus eugenii (ABQO010134790) and Sminthopsis crassicaudata (empty site 2 sequenced in this study using primers F/R4687-55 with a PCR melting temperature of 55 degrees). OC1_Das_NA is present in the Tasmanian devil (position 105–296 of contig GL964687) and is absent from the three other species.

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