A tiny mite with a tinier genome

The sequence of the tomato russet mite’s genome reveals genetic downsizing on a scale never seen in arthropods before.

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

Arthropods are a group of invertebrates that include insects – such as flies or beetles – arachnids – like spiders or scorpions – and crustaceans – including shrimp and woodlice. One of the tiniest species of arthropods, measuring less than 0.2 millimeters, is the tomato russet mite Aculops lycopersici. This arachnid is among the smallest animals on Earth, even smaller than some single-celled organisms, and only has four legs, unlike other arachnids. It is a major pest on tomato plants, which are toxic to many other animals, and it feeds on the top cell layer of the stems and leaves. Tomato growers need a way to identify and treat tomato russet mite infestations, but this tiny species remains something of a mystery.

One way to tackle this pest may be to take a closer look at its genome, as this could reveal what genes the mite uses to detoxify its diet. Examining the mite’s genome could also reveal information about how evolution handles creatures becoming smaller. An area of particular interest is the overall size of its genome. Not all of the DNA in a genome is part of genes that code for proteins; there are also sections of so-called ‘non-coding’ DNA. These sequences play important roles in controlling how and when cells use their genes. In the human genome, for example, just 1% of the DNA codes for protein. In fact, most human protein-coding genes are interrupted by sequences of non-coding DNA, called introns.

Here, Greenhalgh, Dermauw et al. sequence the entire tomato russet mite genome and reveal that not only is the mite's body size miniature: these tiny animals have the smallest arthropod genome reported to date, almost a hundred times smaller than the human genome. Part of this genetic miniaturization seems to be down to massive loss of non-coding DNA. Around 40% of the mite genome codes for protein, and 80% of its protein coding genes contain no introns. The rest of the miniaturization involves loss of genes themselves. The mites have lost some of the genes that determine body structure, which could explain why they have fewer legs than other arachnids. Additionally, they only carry a small set of genes involved in sensing chemicals and clearing toxins, which could explain why they are mostly found on tomato plants.

Greenhalgh, Dermauw et al.’s findings shed light on what may happen to the genome at the extremes of size evolution. Sequencing the genomes of other mites could reveal when in evolutionary history this genetic miniaturization occurred. Furthermore, a better understanding of the tomato russet mite genome could lead to the development of methods to detect the infestation of plants earlier and be highly beneficial for tomato agriculture.