Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution

Marjorie A. Hoy, Robert M. Waterhouse, Ke Wu, Alden S. Estep, Panagiotis Ioannidis, William J. Palmer, Aaron F. Pomerantz, Felipe A. Simão, Jainy Thomas, Francis M. Jiggins, Terence D. Murphy, Ellen J. Pritham, Hugh M. Robertson, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1762-1775
Number of pages14
JournalGenome biology and evolution
Volume8
Issue number6
DOIs
StatePublished - Jan 1 2016

Keywords

  • Dicer-2 gene duplication
  • Genome assembly
  • Helitron rolling-circle transposons
  • Metaseiulus Typhlodromus Galendromus occidentalis
  • Parahaploid sex determination
  • Western orchard predatory mite

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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    Hoy, M. A., Waterhouse, R. M., Wu, K., Estep, A. S., Ioannidis, P., Palmer, W. J., Pomerantz, A. F., Simão, F. A., Thomas, J., Jiggins, F. M., Murphy, T. D., Pritham, E. J., Robertson, H. M., Zdobnov, E. M., Gibbs, R. A., & Richards, S. (2016). Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution. Genome biology and evolution, 8(6), 1762-1775. https://doi.org/10.1093/gbe/evw048