My notes on Plant Biology Europe 2023 at Marseille (day 3)

05072023

Gene DNA methylation in plants: selective pressures and sex chromosome evolution. Aline Muyle.

Most mutations are deleterious. Epigenetics (study of changes in gene expression that can be inherited through cell divisions but are not changes in DNA sequence [Holliday 1987]). This is not Lamarckism (no one has observed env induced epigenetic change so far). CG methylation epimutes over time (rate 1E-4, should be room for selection); depleted in TSS and TTS. CHH methylated genes (upstream) have very low expression. CHG methylation happens at gene bodies [H is A,C,T] and is linked to medium-high expression. Gene body methylation (GBM) is conserved across species, even 300My away, although it is variable [some species don’t have GBM at all, or don’t change expression much when removed (she reanalyzed the data and found the opposite); is it that important then? others have a lot]. GBM methylation evolve slow. She has reviewed all these topics at https://academic.oup.com/gbe/article/14/4/evac038/6550137 , she insists that papers describing them are still highly controversial. So then she tried to measure selection pressure on GBM, with the idea that methylated loci should be removed from populations if GBM is removed. She used for that published methylomes of A. thaliana (n=877, leaf), described at https://pubmed.ncbi.nlm.nih.gov/33871638/, to check whether 4Ns >> 1. She found it is (1.4, comparable to codon usage selection, “tiny effects”) for ancestrally GBM genes [conserved in A. lyrate and C. rubella], but not for all genes. Their hypothesis is that GDM is deleterious for most genes (mutagenic?) and advantageous for a few ones.

She is now working on gene imprinting, which is regulated by methylation and histone marks, that applies to embryos but also in some adult tissues. She is comparing dioecious and hermaphrodite plant species.

Limited water stress modulates expression of circadian clock genes in Brachypodium distachyon roots and induces differential response of proline-metabolism related genes– János GYÖRGYEY

Arabidopsis is a dicot, brachy is much better for monocots. Shows a minimal circadian clock for A. thaliana from https://cshperspectives.cshlp.org/content/8/12/a027748.full to select core clock genes. In his experiments, core clock genes express lower in the roots than in the green parts in most cases (GIGANTEA is the exception, also responds to drought). ELF3/4 expression in the root is not circadian. Under drought, LHY display lower amplitude in expression. PRR95 peaks in root and leaf are a few day hours away.

He then moves to the study of Pro metabolism, a regulatory hub (https://doi.org/10.1016/j.tplants.2021.07.009), is it circadian?  On the shoot [Pro] seems to be circadian, it accumulates during the day and it is consumed during the night.

Two examples of genome-wide evolutionary response of European forest trees to past climate changes– Martin LASCOUX

Little ice age (LIA, 1450-1850). They use a method from Vince Buffalo to look for responses of old forests to IA, which essentially computes allele freq covariation across generations under random drift or under selection (https://www.pnas.org/doi/abs/10.1073/pnas.1919039117). They study 3 oak forests (several cohorts) in France after aging the sampled individuals (https://onlinelibrary.wiley.com/doi/10.1002/evl3.269). They conclude that trees respond quickly, with polygenic responses, as the time frame is only a few generations.