Eukref - Eukaryotic 18S rDNA reference database
The 18S rRNA gene collaborative annotation initiative is a community-wide effort that addresses challenges related to the huge amount of data created by new sequencing techniques with the aim to create useful databases.
About the project and goal
EukRef brings together people with expertise in diverse eukaryotic lineages to curate 18S rRNA gene sequence data using phylogenetic methods. Our goal is to assemble a curated reference database spanning the eukaryotic tree of life. This will be a resource consisting of curated sequences, flexible taxonomy, phylogenetic trees and their underlying sequence alignments. This database will increase the power of high-throughput sequencing-based studies to uncover fundamental patterns in microbial ecology and diversity. Along the way, individual curators are quite likely to identify novel eukaryotic clades and gain new insight into the environmental distribution patterns of eukaryotic microbes.
The team at UiO contributes with a curated database of the microalgal group Haptophyta. This database can be downloaded here.
In 2001 the first clone library based eukaryotic environmental surveys were published using the 18S rRNA gene as a barcode. Since then a lot of studies have used this approach to describe protistan communities in a wide range of environments. The emergence of high-throughput sequencing (HTS) techniques has made this approach even easier to apply. Consequently, the amount of data retrieved has dramatically increased and our knowledge of diversity is ever increasing. But there are pitfalls behind the HTS approaches, which require using, and trusting, reference databases to annotate our data. These databases sometimes contain curation errors and other mistakes that potentially alter our overall view of protistan diversity within and across ecosystems.
Funded by the Gordon and Betty Moore Foundation