The genome of Tetranychus urticae reveals herbivorous pest adaptations

Abstract

The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.

Figure 1. Gene family history

At each time point (grey circles), the number of gains (+) and losses (−) of gene families is indicated as inferred by DOLLOP (black) and CAFÉ (red) programs. The inferred ancestral number of gene families, according to DOLLOP, is shown in green boxes.

Figure 2. Gene expression changes when mites are shifted from P. vulgaris (bean) to A. thaliana or to S. lycopersicum (tomato)

a, A phylogeny of the cytochrome P450 (CYP) genes and heat map of the response of CYP genes to host transfer. Two-thirds of the genes that are tandemly duplicated or that form clusters (indicated by black vertical lines) are co-regulated. b, Global changes in gene expression after host shift. c, Fold changes of important gene family members in digestion and detoxification are colour coded. The analysis of differential expression (b and c) is with a 5% false discovery rate as assessed with RNA-seq data collected in biological triplicate (fold changes between mean values are plotted).

Figure 3. Maximum likelihood phylogeny of the fungal and arthropod carotenoid cyclase/synthase (CS) fusion proteins

The out-group comprises chimaeric assemblies (CSchim) of the closest bacterial sequences of cyclases and synthases. The T. urticae and Acyrthosiphon pisum sequences form a monophyletic group closely related to the zygomycete sequences. Evidence for a single lateral gene transfer event is also shown by the common intron positions in the cyclase/synthase (orange) and desaturase (green) genes (upper right panel). Two clusters of carotenoid biosynthesis genes are found in T. urticae: a tail-to-tail arrangement on scaffold 1 as seen in zygomycetes and aphids, and a more complex head-to-head (re)arrangement on scaffold 11 (bottom right).

Figure 4. Comparative organization of Hox clusters and expression pattern of the T. urticae engrailed gene

a, T. urticae, T. castaneum and D. melanogaster Hox clusters. Gene sizes and intergenic distances are shown to scale. Dashed lines represent breaks in the cluster >1 Mb. In T. urticae, fushi tarazu and Antennapedia are present in duplicate whereas abdominal-A and Hox3/zerknullt are missing (red asterisk). b, Variable pressure scanning electron microscopy (SEM) image of adult T. urticae with two main body regions indicated: P, prosoma; O, opisthosoma. c, T. urticae engrailed (en) expression pattern. en transcripts are detected in five prosomal stripes that correspond to future pedipalpal (Pp), four walking leg (L1–L4) and two opisthosomal (O1 and O2) segments. Scale bars: b, 0.125 mm; c, 40 μm.

Figure 5. T. urticae silk structure and dimensions

a, Spider mite colony on a bean plant forming characteristic silk webbing. b, SEM image of the spider mite larval silk filament (top), and atomic force microscopy (AFM) image of two larval spider mite silk filaments (bottom). c, Height profile of the adult spider mite silk filament obtained from the AFM image. Scale bars: a, 0.75 cm; b, 1 μm.