Open Access Research article

A burst of ABC genes in the genome of the polyphagous spider mite Tetranychus urticae

Wannes Dermauw1*, Edward John Osborne2, Richard M Clark23, Miodrag Grbić45, Luc Tirry1 and Thomas Van Leeuwen1*

Author Affiliations

1 Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent B-9000, Belgium

2 Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA

3 Center for Cell and Genome Science, University of Utah, Salt Lake City, Utah 84112, USA

4 Department of Biology, The University of Western Ontario, London N6A 5B7, Canada

5 Instituto de Ciencias de la Vid y del Vino CSIC, Universidad de la Rioja, Logroño 26006, Spain

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BMC Genomics 2013, 14:317  doi:10.1186/1471-2164-14-317

Published: 10 May 2013

Additional files

Additional file 1:

Midpoint rooted maximum likelihood phylogenetic tree of ABC NBDs of D. melanogaster, H. sapiens and T. urticae. For amino acid alignment, amino acid substitution model and likelihood score of the constructed phylogenetic tree see Additional file 9 and Additional file 10. Main nodes were collapsed to create a better overview of the phylogenetic relationships between the different ABC subfamilies. Numbers at the branch point of each node represent the bootstrap value resulting from 1000 pseudoreplicates (LR-ELW). The scale bar represents 0.5 amino-acid substitutions per site. For accession numbers of metazoan ABC protein sequences see Additional file 11 while T. urticae ABC protein sequences can be found in Additional file 12.

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Additional file 2:

T. urticae ABC fragments.

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Additional file 3:

Exon-intron pattern of 103 T. urticae ABC genes. Exons are depicted as light grey boxes while strandlines represent introns. Within exons red boxes represent NBDs, while small dark grey boxes represent transmembrane helices (TM). Solid arrows indicate direction of transcription.

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Additional file 4:

Phylogenetic analysis of ABCA proteins of five metazoan species, derived according to the procedure in the Figure 2legend.

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Additional file 5:

Identity/similarity matrices between T. urticae, D. pulex, D. melanogaster and H. sapiens ABC proteins. In the upper triangle identity values are shown, while in the lower triangle similarity values are presented.

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Additional file 6:

Phylogenetic analysis of ABCD proteins of five metazoan species, derived according to the procedure in the Figure 2legend.

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Additional file 7:

Phylogenetic analysis of ABCE and ABCF proteins of five metazoan species, derived according to the procedure in the Figure 2legend.

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Additional file 8:

Heat plot of mean expression values (rpkm) of T. urticae ABC fragments from mites on different host plants (bean, tomato and Arabidopsis) and of expression values of T. urticae ABC fragments from four different life stages (embryo, larvae, nymph and adult).

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Additional file 11:

Accession numbers of sequences used for phylogenetic analysis.

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Additional file 12:

103 T. urticae ABC protein sequences (.fasta) (examination of this file requires the BioEdit program (http://www.mbio.ncsu.edu/bioedit/bioedit.html webcite)).

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Additional file 13:

Fold change values of differentially expressed ABC genes of mites after host plant change to either Arabidopsis or tomato.

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Additional file 9:

Alignment of N-terminal NBDs of T. urticae ABC proteins (ABC_N-term_NBD_Tetranychus.fas), N- and C-terminal NBDs of metazoan ABC proteins (ABC_NBD_Metazoa_simple.fas) and of full length metazoan ABCA, -B, C, D, E, F, G and H protein sequences (ABCA-H.fas) (bundled in a .rar file) (examination of the files in this .rar file requires the BioEdit program (http://www.mbio.ncsu.edu/bioedit/bioedit.html webcite)).

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Additional file 10:

Amino acid substitution models used for maximum likelihood phylogenetic analyses and likelihood scores of constructed phylogenetic trees.

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