Sequencing small regions (< 500 bp) of the 18S rRNA gene using Illumina is the standard for environmental sequencing. However, these short fragments have limited phylogenetic information and newly discovered lineages cannot be placed confidently in the tree of life.
Here, we have sequenced the rRNA operon of eukaryotes ( ~ 4500 bp) from three soil samples using PacBio. We have cleaned the reads and now intend to place the lineages in the eukaryotic tree of life using phylogenetic methods. Trees will be constructed using our reads and a curated dataset of taxa representing all eukaryotic diversity.