Genome Sequencing of the Phytoseiid Predatory MiteMetaseiulus occidentalisReveals Completely AtomizedHoxGenes and Superdynamic Intron Evolution

Abstract

Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr of evolution and radically different lifestyles. We present a 152-Mb draft assembly of the M. occidentalis genome: Larger than that of its favored prey, Tetranychus urticae, but considerably smaller than those of many other chelicerates, enabling an extremely contiguous and complete assembly to be built—the best arachnid to date. Aided by transcriptome data, genome annotation cataloged 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. Comparisons with other arthropods revealed a particularly dynamic and turbulent genomic evolutionary history. Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis. Uniquely among examined arthropods, this predatory mite’s Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. Examining gene families linked to characteristic biological traits of this tiny predator provides initial insights into processes of sex determination, development, immune defense, and how it detects, disables, and digests its prey. As the first reference genome for the Phytoseiidae, and for any species with the rare sex determination system of parahaploidy, the genome of the western orchard predatory mite improves genomic sampling of chelicerates and provides invaluable new resources for functional genomic analyses of this family of agriculturally important mites.

Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore

“…2014), and Chelicerata (e.g., I. scapularis and M. occidentalis ; Gulia-Nuss et al. 2016; Hoy et al. 2016) are not representative of all noninsect arthropods.…”

“…2015; Gulia-Nuss et al. 2016; Hoy et al. 2016), the lineage-specific expansions of the TuGR-As and TuGR-Bs within T. urticae are also striking.…”

“…2016) and the predatory mite M. occidentalis (“Gnomon set”, 18,338 proteins) (Hoy et al. 2016) were assessed with HMMER with domain PF00858 (ASC domain).…”

“…Two GR alignments were generated: one containing solely T. urticae GRs (447 intact T. urticae sequences) and one with a representative set of T. urticae GRs from clades A and B, all T. urticae GRs from clade C, 39 intact I. scapularis GRs (Gulia-Nuss et al. 2016), 57 intact M. occidentalis GRs (Hoy et al. 2016), and 58 D. melanogaster GRs (Robertson 2009).…”

“…Intact T. urticae iGluR/IRs (18 sequences) were aligned with those of I. scapularis (Gulia-Nuss et al. 2016) (14 intact iGluR/IRs, and one incomplete IR, IscaIR25a), M. occidentalis (Hoy et al. 2016) (62 intact IR/iGluRs) and a representative set of D. melanogaster iGluR/IRs (Croset et al.…”