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

Abstract

Background: The ABC (ATP-binding cassette) gene superfamily is widespread across all living species. The majority of ABC genes encode ABC transporters, which are membrane-spanning proteins capable of transferring substrates across biological membranes by hydrolyzing ATP. Although ABC transporters have often been associated with resistance to drugs and toxic compounds, within the Arthropoda ABC gene families have only been characterized in detail in several insects and a crustacean. In this study, we report a genome-wide survey and expression analysis of the ABC gene superfamily in the spider mite, Tetranychus urticae, a chelicerate ~ 450 million years diverged from other Arthropod lineages. T. urticae is a major agricultural pest, and is among of the most polyphagous arthropod herbivores known. The species resists a staggering array of toxic plant secondary metabolites, and has developed resistance to all major classes of pesticides in use for its control.

Results: We identified 103 ABC genes in the T. urticae genome, the highest number discovered in a metazoan species to date. Within the T. urticae ABC gene set, all members of the eight currently described subfamilies (A to H) were detected. A phylogenetic analysis revealed that the high number of ABC genes in T. urticae is due primarily to lineage-specific expansions of ABC genes within the ABCC, ABCG and ABCH subfamilies. In particular, the ABCC subfamily harbors the highest number of T. urticae ABC genes (39). In a comparative genomic analysis, we found clear orthologous relationships between a subset of T. urticae ABC proteins and ABC proteins in both vertebrates and invertebrates known to be involved in fundamental cellular processes. These included members of the ABCB-half transporters, and the ABCD, ABCE and ABCF families. Furthermore, one-to-one orthologues could be distinguished between T. urticae proteins and human ABCC10, ABCG5 and ABCG8, the Drosophila melanogaster sulfonylurea receptor and ecdysone-regulated transporter E23. Finally, expression profiling revealed that ABC genes in the ABCC, ABCG ABCH subfamilies were differentially expressed in multi-pesticide resistant mite strains and/or in mites transferred to challenging (toxic) host plants.

Conclusions: In this study we present the first comprehensive analysis of ABC genes in a polyphagous arthropod herbivore. We demonstrate that the broad plant host range and high levels of pesticide resistance in T. urticae are associated with lineage-specific expansions of ABC genes, many of which respond transcriptionally to xenobiotic exposure. This ABC catalogue will serve as a basis for future biochemical and toxicological studies. Obtaining functional evidence that these ABC subfamilies contribute to xenobiotic tolerance should be the priority of future research.

Figure 1

Unrooted phylogenetic tree of N-terminal NBDs of 103 ABC proteins of T. urticae. Amino acid sequences of NBDs were aligned using MUSCLE [122] and subjected to a maximum likelihood analysis using Treefinder [124]. For amino acid alignment, amino acid substitution model and likelihood score of the constructed phylogenetic tree see Additional file 9 and Additional file 10. Numbers at important nodes represent the bootstrap values resulting from 1000 pseudoreplicates (LR-ELW). The scale bar represents 0.5 amino-acid substitutions per site. The different ABC protein subfamilies are indicated by shaded colors. T. urticae ABC protein sequences can be found in Additional file 12.

Figure 2

Phylogenetic analysis of ABCB full and half transporters of five metazoan species: (A) ABCB full transporters, (B) ABCB half transporters. Full-length ABC proteins were aligned using MUSCLE [122] and subjected to a maximum likelihood analysis using Treefinder [124]. The resulting tree was midpoint rooted. For amino acid alignment, amino acid substitution model and likelihood score of the constructed phylogenetic tree see Additional file 9 and Additional file 10. Numbers at the branch point of each node represent the bootstrap value resulting from 1000 pseudoreplicates (LR-ELW). Species, abbreviations, and color codes are: Ce, C. elegans (purple); h, H. sapiens (green); Dm, D. melanogaster (red); Dp, D. pulex (yellow); and tetur, T. urticae (blue). The scale bar represents 0.2 and 0.5 amino-acid substitutions per site in Figure 2A and Figure 2B, respectively. Accession numbers of metazoan ABC protein sequences can be found in Additional file 11 while T. urticae ABC protein sequences can be found in Additional file 12.

Figure 3

Phylogenetic analysis of ABCC proteins of five metazoan species. See the legend of Figure 2 for procedure and display details.

Figure 4

Phylogenetic analysis of ABCG proteins of five metazoan species. See the legend of Figure 2 for procedure and display details.

Figure 5

Phylogenetic analysis of ABCH proteins of five metazoan species. See the legend of Figure 2 for procedure and display details.

Figure 6

Heat map of expression values (RPKM values) of 103 T. urticae ABC genes of mites on different host plants (bean, tomato and Arabidopsis) and from four different life stages (embryo, larvae, nymph and adult). A color legend with corresponding RPKM values is shown at the top of the figure. ABC genes were considered as being expressed when they had an RPKM of >1 in at least one of the spider mite life stages or on one of the plant hosts.

Figure 7

Full length differentially expressed (fold change ≥ 2, FDR adjusted p-value <0.05) ABC genes in mites after host plant change from bean to either Arabidopsis or tomato. Subfamilies are color-coded as follows: ABCA, red; ABCB, yellow; ABCC, green; ABCE, blue; ABCG, purple; and ABCH, brown. Genes found to be significant in only one of the pairwise comparisons have had their fold change values assigned to zero for the non-significant comparison. Fold change values of differentially expressed ABC genes can be found in Additional file 13.