NEW YORK (GenomeWeb News) – In Nature online today, an international research team reported that it has sequenced the genome of a plant pest: the two-spotted spider mite, Tetranychus urticae.
Along with their annotation and analysis of the spider mite's genome the researchers did comparative analyses with other arthropods and incorporated RNA sequence data from spider mites transferred to different plant hosts — experiments that helped them track down genetic and genomic patterns behind everything from spider mite development patterns and silk production to host adaptation and pesticide resistance.
"The analysis revealed mechanisms underlying such diverse traits as pest-plant interactions inspiring novel crop plant protection strategies, and the evolutionary innovation of silk production, presenting opportunities for new nanoscale biomaterial development," co-first author Miodrag Grbic, a researcher affiliated with the University of Western Ontario in Canada and Spain's Instituto de Ciencias de la Vid y el Vino, said in a statement.
The spider mite, named for its ability to spin webs, belongs to an arthropod sub-group comprised of so-called chelicerates and is capable of consuming more than 1,100 plant species. This trait, coupled with its ability to develop resistance to most commonly used pesticides, have made it a potent pest, known for damaging ornamental plants and a range of field and greenhouse crops, from corn or soybean crops to strawberries or tomatoes.
"These mites are often house plant pests — a major cause of people's house plants turning yellow and getting sick," co-first author Richard Clark, a biologist at the University of Utah, said in a statement. "They also are a major problem for agricultural nurseries and greenhouses, and for field crops."
"If we can identify the biological pathways mites use to feed on plants, we can potentially identify chemical and biological methods to disrupt those pathways and stop the mites from feeding," he added.
The international group, which included dozens of investigators from Europe, North America, and South America, used Sanger sequencing to tackle the spider mite's 90 million base genome, the smallest arthropod genome characterized so far.
Along with eight times genome coverage of the London strain of T. urticae, the researchers sequenced expressed sequence tag libraries from embryo, larvae, nymph, and adult spider mites. They also used the Illumina GAII to do RNA sequencing of tissues from Montpellier strain spider mites at different life stages.
The newly sequenced genome appears to house some 18,414 predicted protein-coding genes, including 15,397 genes confirmed by EST, RNA sequence, and/or protein homology data. Researchers also identified 52 potential microRNAs and around 542,600 SNPs or small insertions and deletions in the genome.
Features such as elevated gene density and an abbreviated transposable element repertoire seem to have helped pack these features into the mite's minute genome, researchers explained.
Through comparisons with the genomes of sequenced arthropods from other sub-groups — and with human genomes and cnidarian sequences — the team found nearly 3,000 gene families that are shared amongst the arthropods.
After weeding out genes with homologues in other species, the researchers narrowed in on 4,416 gene families containing more than 6,600 genes that were exclusive to the spider mite. The genome also housed detoxification and digestion genes that were apparently nabbed from bacteria and fungi via lateral gene transfer.
Among the gene families that seem to have undergone changes and expansions in the spider mite genome were some involved in detoxification and breakdown of naturally produced plant defense compounds — features that may help explain the arthropod's broad plant consumption habits and ability to adapt to pesticides.
Consistent with that notion, the team found that detoxification and peptidase genes showed some of the most pronounced gene expression changes in kidney bean-adapted spider mites that were transferred to other host plants such as tomato or Arabidopsis thaliana. Genes with unknown functions, including some predicted to code for secreted proteins, also showed significant expression shifts in the host transfer experiments.
Other spider mite genome analyses offered insights into the repertoire of Hox genes involved in the arthropod's body plan development, the hormone pathway that it uses for growth and exoskeleton shedding, and its silk production method.
In contrast to spiders, which spin relatively thick silk from their abdomen to catch prey, for instance, researchers found that silk production evolved independently in spider mites, leading to a system that allows the mite to produce much thinner silk from its head.
Understanding the silk production system may have applications for those interested in producing biomaterials with similar properties, the study authors noted. The genome is also expected to serve as a resource for those searching for new strategies to protect plants from spider mites and similar pests.