Eukaryotic Identity for Complex Communities
The Tree-of-Life (ToL) chip - an advanced nucleic acid detection tool to assess community structure and diversity of a wide variety of eukaryotic microorganisms within a complex ecosystem.
Image of a ToL phylogenetic chip after hybridization to labeled ITS rRNA amplicons from an environmental DNA sample.
The ToL chip was developed for assessing the taxonomic diversity of eukaryotic microbial communities in environmental samples (soil and sediment). It is based on the Affymetrix GeneChip platform, and includes more than 180,000 total features. The probes were designed to detect oligonucleotides amplified from the internal transcribed spacer 1 (ITS1), 5.8S subunit, and ITS2 segments within the ribosomal operons of genomic DNA from more than 2000 species and strains of fungi, diatoms, and green algae. The ITS regions, which are spliced out of the rRNA transcript during the ribosome maturation process, typically show more sequence divergence than is observed in the ribosomal subunit regions. As such, the ITS regions are often used as taxonomic features for phylogenetic inferences among closely related species of fungi and algae.
Pacific Northwest National Laboratory's general ToL chip is intended to be applicable to a wide variety of aquatic and soil ecosystems. Profiles of ecosystems before and after perturbation are applicable to a wide variety of natural or anthropogenic perturbations.
Contact: Jon Magnuson