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Genome Biol Evol. 2016 Jun 27;8(6):1762-75. doi: 10.1093/gbe/evw048.

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

Author information

1
Department of Entomology and Nematology, University of Florida mahoy@ufl.edu robert.waterhouse@unige.ch stephenr@bcm.edu.
2
Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology The Broad Institute of MIT and Harvard, Cambridge, Massachusetts mahoy@ufl.edu robert.waterhouse@unige.ch stephenr@bcm.edu.
3
Department of Entomology and Nematology, University of Florida.
4
Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland Swiss Institute of Bioinformatics, Geneva, Switzerland.
5
Department of Genetics, University of Cambridge, United Kingdom.
6
Department of Human Genetics, University of Utah.
7
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland.
8
Department of Entomology, University of Illinois at Urbana-Champaign.
9
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine.
10
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine mahoy@ufl.edu robert.waterhouse@unige.ch stephenr@bcm.edu.

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.

KEYWORDS:

Dicer-2 gene duplication; Helitron rolling-circle transposons; Metaseiulus Typhlodromus Galendromus occidentalis; genome assembly; parahaploid sex determination; western orchard predatory mite

PMID:
26951779
PMCID:
PMC4943173
DOI:
10.1093/gbe/evw048
[Indexed for MEDLINE]
Free PMC Article

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