Analyse de la Réponse Evolutive des Arbres forestiers ...Analyse de la Réponse Evolutive des...

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,