1. Evolutionary Biology
  2. Genetics and Genomics

How a tiny tomato pest miniaturises its genome

Scientists have characterised the genome of a tiny tomato mite – the smallest arthropod genome reported to date.
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Scientists have sequenced the genome of a tiny tomato mite that has become a significant agricultural pest, publishing their findings recently in the open-access eLife journal.

A microscopy image of Aculops lycopersici on a leaf of tomato. Image credit: Ronald Ochoa USDA, USA (CC BY 4.0)

The genome of Aculops lycopersici, the tomato russet mite, is the first to be reported for an eriophyoid mite – the smallest plant-eating animal on Earth. At only 32.5 Mb in size, it is also the smallest arthropod genome characterised to date.

Tomato russet mites seem an unlikely threat. These worm-like mites are one of the smallest free-living animals in the world, smaller than some single cells. Its tiny size means it can only feed on the nutrient-poor surface layer of plants and cannot reach the sugar-filled richness of the cells beneath. Nonetheless, it possesses a secret weapon: the ability to manipulate its host’s natural defence systems and rapidly grow in vast numbers. The damage it causes is often overlooked or treated as a microbial disease, but if left to grow unchecked it soon causes the tomato plant to wither and die, turning a russet colour from which the mite gets its name.

“We sequenced the genome of A. lycopersici because it belongs to the Eriophyoidea family, a group of about 4,000 highly derived animal species for which no representative genome was yet available,” explains co-first author Robert Greenhalgh, a postdoctoral fellow at the School of Biological Sciences, University of Utah, Salt Lake City, US. “We were particularly interested in investigating whether its peculiar ecology, such as feeding on a nutrient-poor diet and blocking natural plant host resistance, as well as its derived morphology and small size, could be linked to its genomic makeup.”

The team found that compared to the genome of other arthropods, the russet mite genome was highly streamlined. It had few repeat regions and many fewer ‘introns’ (non-coding regions) within its genes. Nearly 84% of the mite’s genes were intron-less, which is about five times higher than the number of intron-less genes in the common fruit fly, Drosophila melanogaster. It also had 11 times fewer introns than its closer relative, the European house dust mite, which has a genome of about 70 Mb.

Apart from this profound lack of introns, the families of coding genes in the tomato russet mite also deviates from its closest relatives with sequenced genomes, and seems to closely match its streamlined body shape and function. Only a handful of genes have been expanded through evolution in the russet mite, whereas many more have been lost – notably those that are involved in highly conserved biological processes such as protein secretion. There were also many fewer genes acquired from bacteria or fungi, in contrast to the genome of another plant-feeding mite, the two-spotted spider mite Tetranychus urticae. But the most striking loss of genes were those associated with chemosensation, a sensory function, and detoxification. “This makes sense given that the tomato russet mite is mainly found on tomato and that it can suppress the natural defences of its plant hosts,” says co-first author Wannes Dermauw, a former postdoctoral fellow at the Department of Plants and Crops, Ghent University, Ghent, Belgium.

“Our study uncovers genomic features of extreme animal genome reduction, including massive loss of non-coding regions,” adds senior author Merijn Kant, Associate Professor at the Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands.

“The published genome will facilitate comparative studies with other species," concludes co-senior author Richard M. Clark, Professor at the School of Biological Sciences, University of Utah, Salt Lake City, US. "It could also allow for the development of genetic markers for early detection of mite infestations in agriculture."

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    eLife
    e.packer@elifesciences.org
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