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Analyse de la Réponse Evolutive des Arbres forestiers tropicaux dans l’environnement:
Approche génomique et métabolomique
Paris, Fevrier 2016Niklas Tysklind, Gregory Genta-Jouve,
Alexandra Tinaut, Maxime Casalis, Caroline Scotti-Saintagne, Hadrien Lalagüe, Henri Caron, Valérie Troispoux, Saint-Omer Cazal, Marie Pierre Etienne, Celine
Levy-Leduc, Stephane Robin, Sarah Ouadah, Christophe Duplais, Ivan Scotti
Speciation
Savoialen et al, 2006. Nature, 411, 210-213
Species distribution
Species distribution
Allié et al, 2015. PLoS ONE 10(11):
74.5% of Guyanese trees show significant correlations between abundance and elevation
70% of congenerics (14 genera) have species with opposing niche preferences
Symphonia
©RenaultSymphonia globulifera
© Lalagüe©Lalagüe
Symphonia sp1
Two different species?
cpDNA & AFLPs
More gene flow between morphs than at regional level
Phenotypic plasticity?
200920102011201220132014
Reciprocal transplantations
Phenotypic plasticity?
A. B.
P-value=p<0.05P-value<0.001
Phenotypic plasticity?
A. B.
P-value=NSP-value=NS
• suggest trait inheritance and not phenotypic plasticity as the main phenomenon acting here
A. B.
P-value<0.05
P-value<0.05
Phenotypic plasticity?
• Double mechanism explaining the habitat-ecotype association
Gene expression?
EastWest
Hilltops
Bottomland
2 2
22
2
3
3
3 3
3
3
3
22
3
3
EastWest
S.Sp1.
S.glo
S.glo
S.Sp1.
Gene expression?Total RNA cDNA
Illumina Plant total RNA kit (Ribozero)
Norgen Plant & Fungi RNA extraction
3x Illumina HiSeq pair-end 100bp (240 M reads)
LANE 1 LANE 2 LANE 3
Symphonia
W465_3 W476_10 W475_10
W497_2 W424_17 W498_1
M837_23 W475_34 W425_25
W466_27 W497_36 W476_24
M837_14 W424_19 W425_44
W474_4 W475_11 W476_9
M837_39 W424_26 W425_30
W477_42 W474_27 W475_25
W463_27 W497_35 W466_21
M837_12 W424_36 W425_16
W426_20 W503_38 W475_10
W426_16 W503_17 W426_16
W497_3 W497_3 W498_1
W426_36 W426_36 W425_25
W426_7 W503_2 W426_7
Indexing replicates
Lanes 1 & 3
Lanes 1 & 2
12.07 M reads/individual
100 mg 3 leaves
Gene expression?
Gene expression?
45 libraires ont été séquencées
W426_16
W426_36
W497_3
W498_1W425_25
W475_10
No index or lane bias
Gene expression?
Strong grouping by Ecotype, regardless of habitat
Gene expression?Differentially expressed genes by single factors:
• Ecotype differences in gene expression were far larger than among the other factors.
Ecot. Hab. Plant. Prov.
Gene expression?
Ecot. bottom
Ecot.hill
S.Glohabs
S.sp1habs
Differentially expressed genes by interacting factors:
• Each ecotype is expressing genes differently when in the same environment
• homogeneity in gene expression within Ecotype across environments
• Core of genes differentially expressed between ecotypes independent of environment
Gene expression?
• Many other genes differentially expressed depending on environment
Differentially expressed genes by interacting factors:
What about metabolomics?
Metabolomics analysis
Adult babyteen
LC-MS Qtof Agilent 6520 RMN Bruker 600 MHz
PCA analysis of LC-MS data(for the recall)
PLSDA analysis of NMR data
Confusion Matrix: Class: TP FP TN FN
globulifera 0.95238 0.00000 1.00000 0.04762sp1 1.00000 0.04762 0.95238 0.00000
STOCSY analysis of NMR data
Guttiferone AThe PPAP’S family
ID confirmation of the PPAP’s
1H NMR spectrum of the crude latex containing mainly PPAP’s compounds
Cottet et al, 2014 Phytochemistry
Direction of future work:
• Next steps: • ecotype specific polymorphism
• association between polymorphisms/gene expression
• Association between gene expression and metabolites
• Which genes are involved in the speciation process?
• Look at the gene expression of adults (en route):• Is the variance in gene expression between ecotypes the same
as for juveniles?
Acknowledgements:
Alexandra Tinaut
Niklas Tysklind, Gregory Genta-Jouve,Alexandra Tinaut, Kévin Cottet, Maxime Casalis,
Caroline Scotti-Saintagne, Hadrien Lalagüe, Henri Caron, Valérie Troispoux, Saint-Omer Cazal, Marie
Pierre Etienne, Celine Levy-Leduc, Stephane Robin, Sarah Ouadah, Christophe Duplais, Emeline Houël,
Ivan Scotti,
