The Protist Ribosomal Database (PR2)

Laure GUILLOU Station Biologique Roscoff

Diversity and Interactions within the oceanic plankton (DIPO team)

UMR 7144 CNRS, Paris VI

The Syndiniales Amoebophrya ceratii-complex clade 2 infecting Heterocapsa triquetra New chytrid (Dinomyces arenysensis )

infecting Alexandrium minutum

The gregarine Ancora sagittata infecting the polychaete Capitella capitata

Long term dynamic of coastal waters

Nathalie Simon

Polar systems and RCC

Daniel Vaulot

Anne-Claire Baudoux

Marine viruses

Parasites in aquatic systems

Laure Guillou

20 µm

The Roscoff DIPO Team

Fabrice Not

Radiolarians

http://ssu-rrna.org/pr2

Curated taxonomy of unicellular eukaryotes Small SubUnit rRNA and rDNA sequences

Past of the PR2 database

1997 First Database (Daniel Vaulot)

2000

2003

2009

2013

http://keydnatools.com/

http://ssu-rrna.org/pr2

EU PICODIV project (Daniel Vaulot)

Available online databases

(Laure Guillou)

EU Biomarks project (Colomban de Vargas)

French ANR project (Laure Guillou)

The genesis of PR2

• The first embryonic PR2 was created around 1997 by D. Vaulot as an Excel file cataloguing the few hundred algal 18S sequences available at the time

• Unfortunately despite heavy archeological digging, no trace of this file has been found....

EU project PICODIV (2000-2003) Coord. Vaulot Daniel

OLIPAC cruise Nov. 1994

Oslo 2003

Roscoff 2000

Bremerhaven 2002 Bremerhaven 2002

France Spanish England Germany Norway

We miss Colomban!

Access database ARB database Shared between all participants

EU project PICODIV (2000-2003) Coord. Vaulot Daniel

Important numbers of novel eukaryotic lineages

Formal taxinomy

Novel lineages Environmental

sequences

New classification of Eukaryotes Using fixed framework (8 taxonomical fields)

MALV lineages MAST lineages

First problem: environmental sequences

100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800

A

B

A. Sequence AJ010408 (Micromonas pusilla, prasinophyte) B. Squence M88521 (Symbiodinium microadriaticum, Dinophyceae)

V4 region V9 region

100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800

B/A/B A B B Detection of chimera

Second problem: chimera

http://keydnatools.com/

AACTGGTTTAAAGCTTGATTCGTAGCTGCGTTTaAGGGGAAATCGATAGCTT

ACTGGTTTAAAGCTT GGGGAAATCGATAG

SSU rDNA

Small TAGs (Keys)

AACTGGTTTAAAGCTTGccctaGTAGCcgtaaatcTGGGGGAAATCGATAGCTT Species 1 Species 2

ccctaGTAGCcgtaa

Order (1&2) Class (1&2) Species 1 TTCGTAGCTGCGTT Species 2

….. ….. …..

Annotation of environmental

sequences

Automatic generation from referenced database (22501 sequences)

y = 8,7441x - 5558,7 R 2 = 0,8829

80,000

90,000

100,000

110,000

120,000

130,000

140,000

150,000

160,000

170,000

10,000 11,000 12,000 13,000 14,000 15,000 16,000 17,000 18,000 19,000

21 of November 2008

26 of April 2007

Number of sequences in the reference database

Num

ber o

f key

s ge

nera

ted

Last update: August 2012

Ambient Elevated

atmospheric CO2

Fg Ar

Cer

Str M Alv KeyDNAtools

Different annotation 8%

Chimera 19%

Converging annotation 73%

1936 almost complete sequences of 18S From soil (not marine…)

Published

500 sequences per submission

This web site was stopped with the use of NGS technology But was very useful to built a robust, chimera-free, referenced database

http://ssu-rrna.org/pr2

List of experts

in taxonomy + Bioinfo

Curated taxonomy of unicellular eukaryotes Small SubUnit rRNA and rDNA sequences

57 citations in two years

• PR2 is a database made by biologists for biologists

• This is a simple, fast evolving database, which adapts in size and

application to our own scientific projects

THIS IS A TOOL, opens to everyone, but not the central activity of our scientific activity (as SILVA) Updates are time-consuming, requier time and money.

Bacteria, Archaea and Eukaryota

January 2011: same initial database

Silva was not updated using PR2 since 2013 = updates over time are complicated and need a constant effort from experts. PR2: last update in August 2014. TOOLS require for the annotation process/validation need to be simplified

The future of PR2

PR2 Database moved to Roscoff - Fall 2015 (Richard Christen will retire soon).

Work in progress now…

Incorporate novel sequences AND published updates of the taxonomy (alveolates, radiolarians, Chlorophyta, diatoms, haptophytes…) Integration of the EukREF improvment if possible ?

We are preparing a novel update of PR2 for 2015

Future PR2 updates…

Biard et al. (in press) Collodarians

Tragin et al. (in prep) Green lineages Daniel Vaulot Fabrice Not

We will also contact different experts soon (Bente E., Adriana Z. etc..)

Work in progress now… = making our live easier!

2- Upgrade and streamline PR2 web site Downloading new functions, simplification of the PR2 website NGS pipelines (using R) (in fact the tools we are currently using now for

sequence annotation) Metadata (in progress for Prasinophytes)

3- Incorporate NGS database – 2016 (Daniel)

Altran data management company- in progress: 2nd semester 2015

1- New tools to help in database creation and maintenance (functional genes, ribosomal genes, …)

ALL OF THESE UPDATES ARE LINKED WITH OUR RESPECTIVE RUNNING PROJECTS This is probably a critical point for the viability of all databases

Future of the PR2 database?

1997 First Database (Daniel Vaulot)

2000

2003

2009

2013

http://keydnatools.com/

http://ssu-rrna.org/pr2

EU PICODIV project (Daniel Vaulot)

Available online databases (Laure

Guillou) UNIEUK (Colomban)

Diversity; metabarcoding = taxonomy is important BUT how these organisms interact each other is primordial

AQUASYMBIO: a web site database recording all known symbiotic (mutualistic symbioses, parasites, …) interactions in aquatic systems . French ANR project HAPAR (Guillou Laure and Not Fabrice)

AQUASYMBIO (Laure)

Described Interactions

HOST (Species X) AND SYMBIONT (Species Y) Where? When?

Ref

+

Species Z Diagnosis Live cycle Ilustrations Ref

Species X Diagnosis Live cycle Ilustrations Ref

Species W Diagnosis Live cycle Ilustrations Ref

Species Y Diagnosis Live cycle Ilustrations Ref

Species X Species Y Species Z ….

Hosts Symbionts

Interactome

Species description (with Glossary) In progress (1rst release in 2016)