Poster presentation at the Joint Congress on Evolutionary Biology, Montpellier, France, 19-22 August 2018, Symposium 48. Epigenetics and adaptation

1. Joint Congress on Evolutionary Biology, Montpellier, France, 19-22 August 2018, Symposium 48. Epigenetics and adaptation Alexander-Jueterbock@web.de
Poster PDF
Is epigenetic variation the key to success in
seagrass clones?
Jueterbock A1
, Bostr¨om C2
, Reusch TBH3
, Olsen JL4
, Kopp M1
, Dhanasiri A1
, Smolina I1
, Arnaud-Haond S5
, Van de Peer Y6
,
Hoarau G1
1 Marine Molecular Ecology Group, Faculty of Biosciences and Aquaculture, Nord University, Universitetsalleen 11, 8026 Bodø, Norway
2 Department of Biosciences, Environmental and Marine Biology, ˚Abo Akademi University, Artillerigatan 6 FI-20520 ˚Abo, Finland
3 GEOMAR Helmholtz-Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, D¨usternbrooker Weg 20, D-24105 Kiel, Germany
4 Ecological Genetics-Genomics Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
5 Ifremer, Station de S`ete, UMR MARBEC Marine Biodiversity Exploitation and Conservation, Avenue Jean Monnet, CS 30171, 34203 S`ete Cedex, France
6 VIB/Ghent University, Bioinformatics & Systems Biology, Technologiepark 927, B-9052 Gent, Belgium
BACKGROUND AND AIM
Epigenetic stress responses can mediate phenotypic changes that are heritable and,
thus, provide an accelerated pathway for evolution [1]. Evolutionary success of clonal
seagrass meadows with extremely low genetic diversity challenge the hypothesis of
a straightforward relationship between genetic diversity and adaptive potential. We
aimed at testing the hypothesis that variation in DNA methylation, the most stable
epigenetic mechanism [2], is the key to this paradox. Our objectives were to char-
acterize DNA methylation variation in a >1000-years-old clonal meadow [4] and
to identify the role of this variation in heat-stress performance.
METHODS
We sampled 40 seagrass shoots along a transect of >250 meters from a clonal
meadow in the Baltic Sea (Figure 1a). The shoots were grouped into multilocus
genotypes based on 7 microsatellite loci, following [5]).
Heat wave simulation
Sampling times (weeks)
Temperature(◦C)
0 3 8
15
27
a) b)
Figure 1: a) Sampling site and b) heat stress treatment with sampling times.
11 shoots of the seagrass Zostera marina were exposed to heat stress, and
screened for photosynthetic performance (PIABS), [6]) with a PAM fluorometer
at 15◦
C (control), after 3 weeks of stress at 27◦
C, and after 5 more weeks of
recovery back at 15◦
C (Figure 1b).
DNA methylation variation of the shoots was characterized by MethylRAD se-
quencing [7]. MethylRAD is a genome-reduction method based on a methylation-
dependent restriction enzyme that targets CCGG and CCWGG motifs (Figure 2).
Figure 2: Schematic overview of MethylRAD library preparation.
The digested fragments were sequenced with Illumina NextSeq (1x75bp), and
mapped with SOAP [8] to 628,255 MethylRAD tags in silico predicted from the
genome. Clonal variation in methylation was assessed as the mean number
of bivariate methylation differences between all possible pairwise comparisons.
Epigenetic distance between the shoots was assessed as the euclidean distance
along the first two principle components, using the R package ’FactoMineR’ [9].
We tested for correlation between epigenetic distance and stress resilience (rela-
tive photosynthetic performance under recovery) with mantel tests in the R pack-
age ’vegan’ [10].
REFERENCES
[1] Richards CL, et al. (2017) Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. bioRxiv.
[2] L¨amke J & B¨aurle, I (2017). Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol 18, 1 ˜A ˆA ˆA11..
[3] Larkum WD, Orth RJ, & Duarte CM (2006) Seagrasses: Biology, Ecology and Conservation. Springer, Dordrecht, Netherlands 2006.
[4] Reusch TBH, Bostr¨om C, Stam WT, Olsen JL (1999) An ancient eelgrass clone in the Baltic. Mar Ecol Prog Ser. 183:301-304.
[5] Reusch TBH, Bostr¨om C (2011) Widespread genetic mosaicism in the marine angiosperm Zostera marina is correlated with clonal reproduction. Evol Ecol. 25(4):899-913.
[6] Strasser, RJ, Srivastava A, Tsimilli-Michael M & Yunus M (2000) Probing Photosynthesis: Mechanisms, Regulation and Adaptation. (Taylor and Francis, 2000).
[7] Wang S, Lv J, Zhang L, Dou J, Sun Y, Li X, Fu X, Dou H, Mao J, Hu X, Bao Z (2015) MethylRAD: a simple and scalable method for genome-wide DNA methylation
profiling using methylation-dependent restriction enzymes. Open Biol. 5(11):150130
[8] Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics. 24(5):713-4.
[9] Le S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw. 25(1):1-8.
[10] Oksanen, JF et al. (2016) vegan: Community Ecology Package. R package ’vegan’ doi:10.4135/9781412971874.n145
[11] Tiffney BH, Niklas KJ (1985) Population biology and evolution of clonal organisms. in (ed. Jackson JBC, Buss LW, Cook RE) (Yale University Press, New Haven).
RESULTS
Of the 40 shoots, 39 belonged to the same clone. About 75% of the uniquely mapped
MethylRAD-tags fell in intergenic regions, 25% in gene regions, and 41% in transpos-
able elements (either genic or intergenic). Relative performance under heat-stress
recovery was significantly correlated with epigenetic distance in intergenic re-
gions and transposable elements, but not in genes (Figure 3).
Figure 3: Correlation between epigenetic distance in intergenic regions and differences in
photosynthetic performance under recovery from heat stress, in CG and CHG sequence contexts;
p: significance level, R: mantel statistic
Epigenetic distance was independent from geographic distance within the meadow
(p > 0.05). Differential methylation, on average 20-25%, did not differ between
intraclonal and interclonal comparisons. Differences were generally lower in CHG
than in CG contexts (Figure 4).
Figure 4: Proportion of differently methylated sites in the entire dataset (All), in genes, intergenic
regions, and transposable elements, shown separately for CG and CHG sequence contexts, and
for comparisons between shoots of the same clone (intraclone) and shoots of different clones
(interclone).
DISCUSSION
We found that DNA methylation differs between genetically identical seagrass shoots
and was correlated with the ability to recover from heat stress. However, correlation
was only significant for intergenic regions and transposable elements, suggesting that
methylation differences affect gene regulation.
We have demonstrated that DNA methylation variation can partially compensate for
clonality by creating functional phenotypic diversity. Thus, the current reliance on
allelic and genotypic variation alone for management and conservation may be
too narrow to capture stress resilience, stability and adaptive potential of clonal
plants. Given that 40% of all plants reproduce clonally [11], our findings are important
to other fields such as the dynamic of primary producers in general, invasion biology
and crop breeding strategies.
Our next steps will focus on heritability.