Presented during the first EukRef workshop organized in Vancouver, Canada (July 2015).

1. 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

2. 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

3. http://ssu-rrna.org/pr2
Curated taxonomy of unicellular eukaryotes
Small SubUnit rRNA and rDNA sequences

4. 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)

5. 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....

6. EU project PICODIV (2000-2003)
Coord. Vaulot Daniel
OLIPAC cruise Nov.
1994

7. Oslo 2003
Roscoff 2000
Bremerhaven 2002 Bremerhaven 2002
France
Spanish
England
Germany
Norway
We miss
Colomban!

8. Access database
ARB database
Shared between all participants
EU project PICODIV (2000-2003)
Coord. Vaulot Daniel

9. Important numbers of novel eukaryotic lineages

10. Formal
taxinomy
Novel lineages
Environmental
sequences
New classification of Eukaryotes
Using fixed framework (8 taxonomical fields)
MALV lineages
MAST lineages
First problem: environmental sequences

11. 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 AB B
Detection of chimera
Second problem: chimera

12. 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)

13. 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
Numberofkeysgenerated

14. Last update: August 2012

15. Ambient
Elevated
atmospheric CO2
FgAr
Cer
StrM Alv
KeyDNAtools
Different annotation 8%
Chimera 19%
Converging annotation 73%
1936 almost complete sequences of 18S
From soil (not marine…)
Published

17. 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

18. http://ssu-rrna.org/pr2
List of
experts
in taxonomy
+ Bioinfo
Curated taxonomy of unicellular eukaryotes
Small SubUnit rRNA and rDNA sequences

19. 57 citations in two years

20. • 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.

21. Bacteria, Archaea and Eukaryota
January 2011: same initial database

22. 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

23. 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

24. Future PR2 updates…
Biard et al. (in press)
Collodarians
Tragin et al. (in prep)
Green lineages Daniel VaulotFabrice Not
We will also contact different experts
soon (Bente E., Adriana Z. etc..)

25. 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

26. 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)

27. 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)