EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution.

Javier Del Campo,Serafim Nenarokov,Cedric Berney,Laura Wegener Parfrey,Ramon Massana,Martin Kolisko,Vittorio Boscaro,Matthew W Brown,Colomban De Vargas,Alastair Simpson,Laure Guillou,Patrick J Keeling,Luciana F Santoferrara

doi:10.1371/journal.pbio.2005849

Abstract

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, the European Nucleotide Archive [ENA], or the DNA DataBank of Japan [DDBJ]), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases.

Highlights

Most lineages of eukaryotes (organisms with nucleated cells) are microbial, and eukaryotic diversity extends far beyond the familiar plants, fungi, and animals
Most lineages of eukaryotes are microbial, and eukaryotic diversity extends far beyond the familiar plants, fungi, and animals
The term “protists” describes a polyphyletic assemblage, it was widely used for convenience to describe the smallest size fraction of eukaryotic organisms, delineating them from bacteria and archaea

Summary

Introduction

Most lineages of eukaryotes (organisms with nucleated cells) are microbial, and eukaryotic diversity extends far beyond the familiar plants, fungi, and animals. The final outputs of EukRef for each group are (1) a phylogenetic reference tree and alignment, (2) a curated reference database with accession numbers, curated classification string, and curated metadata, and (3) a list of sequences known to be problematic (such as chimeras).

Results

Conclusion