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.

 

 

My notes on Plant Biology Europe 2023 at Marseille

Hi, in this and following posts I will be sharing my notes of the sessions of the Plant Biology Europe 2023 at Marseille: https://europlantbiology2023.org

day2 day3 day4

Note: access here the slides of the "Learning to build and interrogate the pangenome of Brachypodium distachyon" talk.

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Uncovering the hidden half of plants: discovering novel ways roots sense and adapt to heterogeneous environments. Malcolm Bennet.

Talks about xerobranching (https://pubmed.ncbi.nlm.nih.gov/30270188), a mechanism to control root branching in water-deprived soil layers. This is initially controlled by phloem-produced ABA [compamion cells] that travels to the root and triggers an auxin response in the epidermis [plasmodesmata] (https://doi.org/10.1126/science.add3771). They have used air-gap experiments to show this is conserved across angiosperms.

In the 2^nd part of the talk he talks about how soil compaction inhibits root growth and produces actually wider roots. However, in mutants unsensitive to ethylene, roots can actually overcome compaction. It seems that growth arrest is actually an ethylene response. Plants sense compaction by gauging gaseous ethylene diffusion in the soil (root radar signal). He is asked whether growing through compact soil actually damages the root. His answer is that natural variability suggests that damage is not the main driver or these mechanisms.

He goes on to stress we need to consider plant + soil + microbes to answer any root questions, so we should all talk to soil and microbe scientists.

 

A central role of root symbionts: the plant response to environmental stresses. Raffaella Balestrini.

Explains how strigogalactones produce by the root trigger the fungus infection during mycorrhiza establishment. Transcriptional landscape changes before -> after, revealing that [plant, fungus]  redundant transcripts encoding P-transporters ate upregulated. She shows experiments with Lotus japonica + Gigaspora. She moves to explain that AM symbiosis increases drought resilience, but it’s a process we still know little about, as responses depend on genotype interactions. She mentions https://doi.org/10.1126/science.aaz5192 and https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18281. She explains that infection in tomato affects also stomata density.

They are now working in a consortium that will produce tomato seeds coated with priming chemicals [including salicylic acid, which affect spore germination] and fungal spores to maximize stress resilience of adult plants.  She mentions https://doi.org/10.1016/j.tplants.2022.06.004 .

 

Fusing genome simulation and crop models for computer-aided breeding in future environments – Arnaud DESBIEZ-PIAT

Talks about training genomic prediction models with 10-cross validation as part of a virtual breeding platform. They get the genotypes ranked correctly, but has a 3d biass in anthesis date. Explores the effect of simulated and real recombination and models (rrBLUP vs Bayes) on the correlation of traits. He says that automatic phenotyping of germination rates is very hard. The goal is to keep genetic gain > errors.

Pervasive Under-Dominance in Gene Expression Underlying Emergent Growth Trajectories in Arabidopsis thaliana Hybrids– Wei YUAN

As Daniela Ristova, uses Biorender.com to make summaries. In her experiments comparing F1 hybrids to inbreds she finds less additive genes than dominant ones [hybrids have larger rosette areas]. She finds that promoters with more rare alleles have lower expression [allele freq as a proxy of deleteriousness], with hybrids with less rare alleles performing best. Paper soon out in Genome Biol?

Reconsidering photoperiod-sensitivity (PS) for maize adaption to climate change– Justine DROUAULT

Hypothesis: tropical maize could be re-introduced into temperate maize to increase adaptation in the face of climate change. She shows that selection towards PS indirectly selected also for other traits, such as plant height, etc. She classifies haplotypes according to their PS. She finds that tropical genotypes can reduce thermal time to flowering, but effect depends on background genotype.

Plasticity of root permeability for nutrient acquisition. Marie Barberon.

She explains the plastic role of suberin diffusion barrier in the root, citing https://www.pnas.org/doi/10.1073/pnas.2101730118.  A set of at least 4 MYB factors control (ectopic) suberization: 41,53,92,93. They cannot do single-cell as they cannot produce viable protoplasts of their root cells.

Polygenic selection and the evolution of gene expression in Arabidopsis Iyrata. Juliette de Meaux.

Inspiring talk on how her group is taking advantage of the Arabidopsis genomes (thaliana, halleri and lyrata) to study gene dominance. She starts by explaining that most genetic variance is deleterious and probably cannot be removed due to drift and the inability of selection to eliminate it. She shows that genes that show dominance display less Ks (more constrained) and that, conversely, additive genes, with smaller phenotypic effects, show larger Ks values (https://europepmc.org/article/ppr/ppr453330). She refers to https://www.nature.com/articles/s41467-021-23558-2, where they compare sterile hybrids of those species to classify cis variation. In outlokk, she favors future focus on many genes with small additive effect but large collective weight.

Changes in competitive ability over the course of durum wheat domestication are mediated by plant functional traits– Taïna LEMOINE

She studies Triticum monococcum, T. dicoccoides, T. turgidum landraces and T. turgidum elite varieties to measure their i) performance and ii) trait plasticity in the face of stress. She finds that domesticated materials performs better overall, but in terms of individual trait plasticity, wild material show larger variability, which suggests that breeding with a view of individual traits can still make gains from wild materials.

Horizontal gene transfer in Hordeum species– Marek SZECÓWKA

Hordeum species acquired DNA from panicoid sources via at least 9 events 5-1My ago. These lineages diverged 50Myr ago (https://pubmed.ncbi.nlm.nih.gov/33484020/). He asks how many accessory genes are from panicoids and what are their roles. So he chops Hordeum  genomes in 1Kb bits which are then mapped onto reference panicoid genomes, requiring at least 500b matches (BLASTN, 175b for BLASTX) and high % identity. He then requires >=70% identity and fragments >=5Kb for further analysis.  

They have also tracked panicoid TEs in Hordeum genomes and they seem to follow the segments and chromosomes previously shortlisted. They behave effectively as additional confirmation. They have built consensus panicoid TE library for this work.

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Janet Thornton, se jubila la madre de la bioinformática estructural

Hola, ayer escuché por videoconferencia un rato de la última charla que dio Janet Thornton en el EMBL-European Bioinformatics Institute antes de jubilarse.

fuente: EMBL

Janet ha sido sin duda una de las madres de la bioinformática, sobre todo en el área de la bioinformática estructural. Por ejemplo, tiene su propio modelo de sustitución de aminoácidos para hacer filogenias (JTT). Podéis ver su enorme influencia en la literatura en EuropePMC, o las palabras que le dedican Alfonso Valencia o Roland Dunbrack. Entre la larga lista de discípulos están por ejemplo David Jones (la J del modelo JTT, parte del equipo de AlphaFold y examinador de mi tesis), Christine Orengo o Nick Luscombe, todos ellos autores a los que he citado innumerables veces.

Yo la conocí personalmente en un congreso en Brasil, el ISMB2006, donde tuve la fortuna de tener una reunión cara a cara con ella donde me dio consejos y ánimos para mi incipiente carrera en la ciencia. Hace 4 años volvimos a coincidir en la cafetería del EMBL-EBI y recordando ese rato me dijo algo como "no te ha ido tan mal, verdad?".

En su charla recordaba observaciones que ella y su grupo habían hecho en las últimas décadas sobre la lista de aminoácidos importantes para explicar la catálisis de las enzimas. Eso le dio pie a repasar los resultados de los últimos años de trabajo, liderados por Antonio Ribeiro, donde se han centrado en sistematizar las reglas y en medir de manera objetiva la similitud entre mecanismos enzimáticos, ganando capacidad predictiva por el camino (ver por ejemplo https://europepmc.org/article/MED/36659981 y https://europepmc.org/article/PPR/PPR540240). Terminó esta parte de la charla, la última que pude seguir, diciendo que lo más difícil de jubilarse era no poder planear nuevos experimentos y estudios para todo lo que queda por saber. Creo que esa curiosidad es el motor para muchos de nosotros, no tengo nada más que añadir,

hasta pronto,

Bruno

 

 

 

 

 

Aprende Bioinformática en España en 2023

Hola,

hoy comparto un documento que ha publicado la asociación de jóvenes bioinformáticos de Granada (BioInfoGRX).

Se trata de la guía "Aprende BioInformática", que se ocupa de:

• Estudiar BioInformática en España (grados y másters)
  
• Cursos online de BioInformática (biología, programacion y analisis de datos)

Es un documento dinámico que actualizará su contenido periódicamente. Puedes sugerir cambios en bioinformaticsgrx@gmail.com y descargarlo en:

https://bioinformaticsgrx.es/wp-content/uploads/2022/02/Gui%CC%81a-formativa-en-bioinforma%CC%81tica.docx.pdf

Espero sea útil,

Bruno