My notes on Plant Biology Europe 2023 at Marseille (day 4)

 06072023

How to conquer a plant using just eight genes: learning from geminiviruses. Rosa Lozano-Duran

Geminiviruses (n>=9 coding genes, splicing enabled) have a very high mutation rate despite being replicated by the host plant system, probably because they force the use of their own polymerase subunit. The most divergent protein in these viruses is C4; it also has several transit peptides, including a sp signal, and it is sufficient and required to elicit infection symptoms [including drought tolerance]. C4 interacts with RLD proteins. Their experiments found that symptoms and viral performance can be uncoupled with the right mutations.

Evolution of cooperation in post-green revolution durum wheat cultivars– Michel COLOMBO

Have we bred weaker competitors after the green revolution? Plots with both low and high density of two genotypes. He confirms this idea and then asks whether we need to continue this trend with current conditions in Montpellier.

Chromatin regulation of and by gene islands in plants– Louis-Valentin METEIGNIER

His work is about the expression of biosynthetic pathways (benzoxazinoids, known to inhibit histone deacetylases) that he suspects have an effect on the performance of intercropping. He mentions recent papers on this hot topic (https://doi.org/10.1073/pnas.2201886120). He intercrops rice and maize, co-planted for 3 weeks (https://dx.doi.org/10.1073/pnas.2001290119).

Identification of genes and metabolites controlling plant-plant interaction (Allelopathy)– Sophie JASINKSI

Adequate varieties should be used to avoid allelopathy affecting performance [often hard to tell from simple competition]. She is carrying out GWAS and Metabolite-WAS [root exudates] analyses in this topic with A. thaliana. She has access to the phenoscope to test a variety of donor (n=385) and receptor (Col-0) accessions. She can observe phenotypic variation. Suspect compounds include glusinolates [aliphatic vs indolic], coumarin, so she looked at candidate genes in these pathways.

Molecular bases of plant-plant interactions: identification of the molecular pathways depending on ESC-1, a RLK involved in the competitive response in Arabidopsis thaliana– Marie INVERNIZZI

91 accessions, 3 species (Poa annua, ) from a French population that compete with A. thaliana.She finds that ESC-1 [naturally variable] plays a role in this competition [some experiments still running], which changes according to stress responses according to transcriptomic data. Arabidopsis senses the competition likely through root exudates.

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

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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.

My notes on Plant Biology Europe 2023 at Marseille (day 2)

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Davide Bulgarelli's dream of personalized agriculture, inspired by personalized medicine.

 

 

 

Getting organised – the (re)evolution of fertility after genome duplication. Kirsten Bomblies.

Increased chr number -> increased cell size, this might affect organs such as stomata or xylem architecture. WGD might be a promising tool in agriculture, but often causes sterility (neo vs evolved polyploids). Her lab investigates how polyploids evolve using Arabidopsis thaliana and arenosa, that allow you to see the stages of polyploidization (https://royalsocietypublishing.org/doi/full/10.1098/rspb.2020.2154). She uses genome scan for selection, where allele freqs are plotted vs genome position, to find genes selected after polyploidization. 

Story 1 (fwd genomics of adaptation). Chiasmata formation in meiosis. They found that A. arenosa has amore efficient and lower crossover rate than neotetraploids (https://doi.org/10.1016/j.cub.2021.08.028 , https://doi.org/10.1073/pnas.1919459117).

 Story2 (rev genomics). Sterility of neopolyploids. They found genes under selection active during pollen tube formation (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8623246/).

P-bodies and post-transcriptional gene regulation in plant reproduction and stress response.  Karel Riha.

Describes their work on using microscopy and mutants to study the transition from meiosis to mitosis in gametogenesis in Arabidopsis thaliana (https://elifesciences.org/articles/52546 , https://www.frontiersin.org/articles/10.3389/fpls.2018.01602/full , https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009779). This transition requires suddenly stopping translation (https://pubmed.ncbi.nlm.nih.gov/35926014/).

The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements– Francois PARCY

UFO + LEAFY bind to specific LUBSO cis elements, which are a subset of those bound by LEAFY, as revealed by DAPseq. They found both monomeric and dimeric sited that contain half/entire  LEAFY sites plus an UFO site. They still don’t know whether UFO directly contacts DNA. They have also found that LEAFY K249 is crucial for the interaction with UFO + ubiquitination complex (https://pubmed.ncbi.nlm.nih.gov/36732360/). There hundreds of F-box proteins in A. thaliana, others might be doing the same, modifying targets of other TFs.

Timely endosperm elimination in Arabidopsis requires a programmed cell death pathway regulated by NAC transcription factors– Nicolas M. DOLL

Programmed Cell Death, controlled by several NAC transcription factors, plays a role in the embryo growth (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4453791). They saw that 4x NAC mutants (KIR1 and the others) produce larger, misshapen seeds, where the embryo does not take all the usual volume. These NACs are expressed in other tissues in the context of cell death (ie stigma development).

Predictable gene editing through Prime Editing in model plants and potential for crop breeding– Fabien NOGUE

Cas9 double-strand nicks phenotypes cannot always be predicted as they depend on subsequent DNA repair. Prime editing from 2019 allows susbtitutions and indels and has lower efficiency than Cas9 or base-editing tools. Needs to be improved for use in crops. He uses Physcomitrium as a model, which already has a T2T assembly, and the APT reporter gene. In their hands, prime editing was initially 30x efficient than Cas9 (https://pubmed.ncbi.nlm.nih.gov/35151447). Their strategy was to i) protect the PegRNA by fusing to it a viral pseudoknot [works], ii) use another reverse transcriptase [did not work], iii) split the nCas9 and RT in two proteins [a bit weaker]. They have now benchmarked their approach in A. thaliana, soybean, potato and grape, reporting an efficiency 2.5x smaller than classical Cas9.

CRISPR-based tool development to engineer plant genomes at the megabase scale– Júlia ARRAIZA RIBERA

She talks about her PhD OMEGA project where she uses P. patens to test Mb-scale, Cas9-dual targeting editions of the genome. Her goals are i) 5-10% genome reduction and ii) site-specific recombination. They find that large deletions (up to 100Kb) work in simplex, she is now testing multiplex epxeriments.

She is also testing Cre/lox to induce recombination, which requires inserting in the genome the loxPsym sites with CRISPR [works as expected in simplex, but tricky in multiplex settings or when sites are nearby on the same locus]. Recombination experiments to come.

Arabidopsis thaliana natural variation for photosynthesis: a model to guide improving crop photosynthesis? Mark Aarts.

Rubisco evolved when there was no much [O2] and suffers competition from oxygen in today’s conditions. Yield potential is a function of solar irradiance, interception efficiency (improved by breeding), harvest index (improved by breeding) and conversion efficiency into biomass (no targeted by breeding, potential for improvement, refers to Steve Long). Photosynthesis can be measured with gas analyzers, low throughput. Fluorescence imaging is much better for scaling up (ie MultispeQ), but this only a proxy for CO2 fixation, which is the real target. They have found natural variation for photosynthesis and and particular genes such as PPR YS1 (https://doi.org/10.1104/pp.114.252239) or Squalene epoxygenase-line (SQE) genes that have gained/lost exons and promoters across ecotypes and affect PSII performance. SQE are unique to Brassicaceae and Cleomaceae. There is also genetic variance in the cytoplasm, they have a protocol to swap plastids (https://www.nature.com/articles/s41477-019-0575-9). They then tested a set of plastotypes and measured their photosynthesis rates, finding a couple of outstanding plastotypes with mutations in cp gene ndhG. Overal so far they have documented 7 genes with natural variation related to photosynthesis efficiency (diff alleles contribute to a few % points of PS). He terminates by advertising the new Jan IngenHousz institute in Wageningen. Heritability of PS is 30% in optimal conditions, higher if you challenge the plants.

 

Comparative genomics session

1. The first pan-genome of a non-vascular plant broadens the understanding of land plants adaptation to their environment – Chloé BEAULIEU

Chloé is a 3rd year PhD student at the LRSV in Toulouse, in the EVO team lead by Pierre-Marc Delaux. She’s working on the genetic diversity of non vascular plant Marchantia polymorpha, in order to develop better knowledge of non-angiosperms. The overall goal is get new insights into the adaptation of landplants to their environment. Core < 10k genes acros > 100 ecotypes

2. Adapting CRISPR from Physcomitrium patens to sexually dimorphic moss, Ceratodon purpureus – Emilie-Katherine TAVERNIER

Emilie completed her PhD just two weeks ago. She has been working with the dioecious moss Ceratodon purpureus to evaluate sex linked genes. In this presentation, she’ll be tell us about about how she established CRISPR-Cas9 in tha species and some of the molecular barriers she had to overcome. 5x less efficiency than Physcomitrium. She won't talk about her latest upublished results.

3. The evolution of Arabidopsis centromeres – Fernando RABANAL

Fernando got a genomic sciences degree at UNAM, where I was fortunate enough to teach for some time. He became fascinated by the mysteries entangled in the repetitive fraction of the genomes since his PhD studies at the Gregor Mendel Institute in Vienna, where he investigated the natural variation and epigenetic regulation of ribosomal RNA gene clusters in A. thaliana with NGS data. Aware of the limitation of short-read data, for his postdoctoral research, I chose a group at the forefront of long-read sequencing technologies at the Max Planck Institute for Biology Tübingen. There he has been able to mine what has traditionally been inaccessible ‘dark matter’ in plant  genomes, namely, centromeres ribosomal RNA gene repeats. 10% innaceasible genome with HiFi. software for annotation:  https://academic.oup.com/bioinformatics/article/39/5/btad308/7159186

4. Divide and conquer: Evolutionary adaptations of the plant cytoskeleton during cell division – Katharina BÜRSTENBINDER

Her lab studies evolutionary adaptations and plant-specific functions of the cytoskeleton and she explain in depth recent, published work discovering a family of proteins involved in controlling cell divisions in plants that grow in 3D. This family expanded in angiosperms but goes back to some fungi (https://pubmed.ncbi.nlm.nih.gov/37068357).

 

Mural enfrente de la estación de Marsella.