Eukaryotes in the Silva database

Laura Wegener Parfrey Knight lab, CU Boulder

Pelin Yilmaz – MPI Bremen Silva in general

• SSU and LSU rDNA only • Curated based on alignment, sequence quality metrics and length (reference sets greater than 1200 bp) Silva 108 • Qiime formaed files currently available (from Qiime.org resources) • Tony Walters implemented 18S tutorial

Problems with Silva 108

• About 1/5 listed as uncultured eukaryote • Taxonomy based on NCBI • Not standardized for computaonal analyses – Variable numbers of levels/ranks – Tony generated RDP formaed taxa maps – but just grab first categories Eukaryoc Taxonomy Working Group

• Collaboraon between Silva ribosomal database (Pelin Yilmaz), ISOP systemacs commiee and others with computaonal or taxonomic experse. • Goals for the revised classificaon – reflect phylogeny – Interface with computaonal tools

Pelin Yilmaz and Frank Oliver Glockner Eukaryoc Taxonomy Working Group

• Revised classificaon based on ISOP taxonomy (Adl et al 2005 and updates) – Implemented in the Silva 111 release • Other databases (Greengenes and RDP) also commied to incorporang eukaryotes in next release. Eukaryoc Taxonomy Working Group

• Collaboraon between Silva ribosomal database (Pelin Yilmaz), ISOP systemacs commiee and others with computaonal or taxonomic experse. • Goals for the revised classificaon – reflect phylogeny – Interface with computaonal tools Silva 111

• 71787 eukaryoc sequences • 13582 fungal sequences • Taxonomy assigned to uncultured sequences according to tree (e.g. uncultured ciliate rather than uncultured eukaryote) Silva 111 – taxonomy sources

• Deep eukaryotes and prosts – ISOP (Internaonal Society of Prostologists) classificaon Silva 111 – taxonomy sources Summary

451 taxa, 72 lineages

16 genes

Parfrey et al. 2010 Silva 111 – taxonomy sources

• Deep eukaryotes and prosts - ISOP classificaon • Fungi – originally Pelin using Index Fungorum – Currently looking into Mycobank – Ideal: adopt same taxonomy as ITS database • Long term: aim to sync taxonomy with other efforts, e.g. Open tree of life project Silva 111 – taxonomy

• Also released flat file of taxonomy • Encourage users to use taxonomy of choice • Customize ranks (for RDP classifier) based on study Silva 108 curated tree

Animals

Fungi

Amoebozoa Excavata

Alveolates

Stramenopiles

Rhizaria Green algae (plants)

Red algae Topiary Explorer Visualizing the high-throughput sequencing data within a phylogenec context

Developer: Meg Pirrung in Knight lab hp://topiaryexplorer.sourceforge.net/

A) Eukaryotic tree colored by taxonomy Environmental sequences B) Eukaryotic tree colored environment Rhizaria colored by clade

Stramenopiles Blastocystis

Ciliates

Green algae

C) Bacterial tree colored by environment Enterobacteria

Proteobacteria

Candida Fungi important in Fungi Tenericutes most environments. Actinobacteria Bi!dobacteria Prevotella Bacteroidetes

Acidobacteria

Animals Firmicutes

Closteridia

Entamoeba Amoebozoa Lactobacillus

Parabasalids Archaea Example of ranks file

Path node_name rank_name level Eukaryota Eukaryota domain Level 1 Eukaryota;Amb-18S-6341 Amb-18S-6341 phylum Level 2 Eukaryota;Amoebozoa Amoebozoa kingdom Level 2 Eukaryota;Amoebozoa;Archamoebae Archamoebae phylum Level 3 Eukaryota;Amoebozoa;Archamoebae;Entamoebida Entamoebida order Level 4 Eukaryota;Amoebozoa;Archamoebae;Entamoebida;Entamoeba Entamoeba genus Level 5 Eukaryota;Amoebozoa;Archamoebae;Mastigamoebaea Mastigamoebaea order Level 4 Eukaryota;Amoebozoa;Archamoebae;Mastigamoebaea;Mastiga moeba Mastigamoeba genus Level 5 Eukaryota;Amoebozoa;Cavosteliida Cavosteliida class Level 3 Eukaryota;Amoebozoa;Cavosteliida;Cavostelium Cavostelium genus Level 4 Eukaryota;Amoebozoa;Cavosteliida;MPE1-14 MPE1-14 order Level 4 Schizoplasmodio Eukaryota;Amoebozoa;Cavosteliida;Schizoplasmodiopsis psis genus Level 4 Eukaryota;Amoebozoa;Cavosteliida;Tychosporium Tychosporium genus Level 4 Eukaryota;Amoebozoa;Dictyostelia Dictyostelia class Level 3 Eukaryota;Amoebozoa;Dictyostelia;Acytostelium Acytostelium genus Level 4 Eukaryota;Amoebozoa;Dictyostelia;Dictyostelium Dictyostelium genus Level 4 Eukaryota;Amoebozoa;Dictyostelia;Polysphondylium Polysphondylium genus Level 4 Eukaryota;Amoebozoa;Discosea Discosea phylum Level 3 Eukaryota;Amoebozoa;Discosea;Flabellinia Flabellinia class Level 4

Eukaryota;Amoebozoa;Discosea;Flabellinia;Dactylopodida Dactylopodida order Level 5 Eukaryota;Amoebozoa;Discosea;Flabellinia;Dactylopodida;A1W VB A1WVB family Level 6 Eukaryota;Amoebozoa;Discosea;Flabellinia;Dactylopodida;Koro tnevella Korotnevella genus Level 6 Eukaryota;Amoebozoa;Discosea;Flabellinia;Dactylopodida;Neo paramoeba Neoparamoeba genus Level 6 Eukaryota;Amoebozoa;Discosea;Flabellinia;Dactylopodida;Pse Pseudoparamoe udoparamoeba ba genus Level 6 Eukaryota;Amoebozoa;Discosea;Flabellinia;Dactylopodida;Vexil lifera Vexillifera genus Level 6 Release of Qiime formaed files

• Later this fall • 99% and 97% representave sequences – Aligned and unaligned – Genbank accession is the idenfier • Taxa map – Full – RDP formaed • Tree for eukaryotes only How to integrate ITS and 18S based classificaon / databases?

Collaborators: Rob Knight (CU) Acknowledgements Pelin Yilmaz (Silva) Frank Oliver Glockner (Silva)

Knight Lab: Tony Walters Matt Gebert Chris Lauber Daniel McDonald Jose C Clemente Scott Bates Jessica Metcalf

Eukaryoc taxonomy working group