Tom Raaymakers

Save the CSIRO

Our national science & research agency is now facing more job cuts than under Tony Abbott

Call on the Albanese Govt to fund the scientists & research we need to tackle big issues we face from climate to food security and everything in between

www.davidpocock.com.au/save_our_csiro

Postdoc position in my lab in Cologne starting early next year or latest in spring to get this exciting project started.

jobportal.uni-koeln.de/ausschreibun...

1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!

Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...

The early bird 🐥 registration for the 8th International Bacterial Wilt Symposium has been extended until the 15th of November! To join those who have already registered visit our website 👉https://event.wur.nl/ibws2026

DNA-free RNA isolation protocols for Arabidopsis thaliana, including seeds and siliques - BMC Research Notes Background High throughput applications of the reverse transcriptase quantitative PCR (RT-qPCR) for quantification of gene expression demand straightforward procedures to isolate and analyze a conside...

In my previous lab this method was often used as a cheap alternative to commercial kits: bmcresnotes.biomedcentral.com/articles/10.... but don't know how well it would translate to your samples

Engineering the C-tail of the versatile Arabidopsis immune receptor RLP23 enhances pathogen resistance in rice and poplar!
Congrats to Andrea Gust and her group at #ZMBP 👏👏👏
#MPMI #EvoMPMI #plantsci

Pervasive splicing in a plant DNA virus https://www.biorxiv.org/content/10.1101/2025.10.01.679800v1

Great job by Erin for her first ever oral presentation. #SOLRUB2025 Our paper describing part of the work presented can be found here: link.springer.com/article/10.1...

Autocycler: long-read consensus assembly for bacterial genomes AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

Assistant Professor of Plant Pathology University of California, Davis is hiring. Apply now!

My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339

Genetic suppressors of the growth‐immunity trade‐off in the Arabidopsis salicylic acid‐accumulating dmr6 dlo1 mutant This study reveals genetic factors underlying the salicylic acid (SA)-mediated growth-immunity tradeoff in plants by identifying suppressor mutants with restored growth in the background of the highl...

The latest paper from our work on DMR6. Genetic suppression of growth reduction in the Arabidopsis dmr6_dlo1 mutant. Results of the forward genetics screen by Tijmen van Butselaar💪🏻. Interested… read the paper😄. onlinelibrary.willen.com/doi/10.1111/...

Congratulations!

Yeah it's become so easy to get high quality (bacterial) genomes now. Fungal genomes are a bit more tricky I guess. Especially those pesky rusts.

Sure, but it’s still early days and this was the first bacterial plant pathogen sequenced (as far as I know, though some Xanthomonads and Xylella appeared soon after). We plant pathologists do crave a bit of recognition! 😉

Also 4 plant pathogens in the top 100 seems about right 🙃

List of bacterial genomes available at NCBI datasets ordered by date, oldest first, the Ralstonia genome is at #25 out of close to 3 million genomes

Still being in the top 30 out of almost 3 million bacterial genomes available now ain't bad 😁

+the green revolution

PhD Position on Decoding Plant Microbiota–Host Specificity Using AI Join us to generate data and build AI-driven models to decode plant–microbiota host specificity!

One more week to apply for an open PhD position in my team at Utrecht University. Interested in genetics, genomics, bioinformatics, microorganisms and plant-microbiota interactions, don't hesitate and apply! www.uu.nl/en/organisat...

Ruige zegge (Carex hirta)?

The EPS-I exopolysaccharide transforms Ralstonia wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta Ralstonia solanacearum species complex (RSSC) pathogens cause destructive plant wilt diseases of a wide variety of crops, leading to significant agricultural losses worldwide. These bacteria rapidly s...

Direct link to our pre-print www.biorxiv.org/content/10.1...

or you can skim the tweets below --

So -- What are Ralstonia and why are they goopy?

Ralstonia are bacterial pathogens of plants. They colonize and clog the water-transporting xylem vessels, causing rapid-onset wilt disease—they can fatally wilt plants within days.

This timelapse by Jonathan Jacobs shows a sped-up time-course.

Just in time to add it to our manuscript (hopefully submitted soon 🙂)

It is! Almost instant as opposed to hours previously 😃

I have raised the issue on the pyani-plus git, also a question about the number of log files, which maybe by design :)

Plant pathogens getting funky

my assembly pipeline creates .fa files, renaming them was not a big issue, but would be nice to have .fa included too.

I hope that the database lookup goes quicker than pyani0.3.0-alpha, when adding genomes to an ANIm database the calculation of which new comparisons needed to be made took ages (don't know if this is a me problem though :))

Give it a go with sourmash first (because it's quick :)) with ~350 genomes, looking very spiffy! Results looks very similar to ANIm. I will run all methods over the weekend just to compare the outputs.

Looks awesome, will give it a try soon 😊

Super cool #bioinformatics tool alert: @widdowquinn.bsky.social group releases PyANI-plus, a flexible tool for exploring whole-genome similarity on large AND detailed scales. Walkthrough available below!