Professor in Epidemiology/Pathology for Agricultural Crop Plants - Ledig stilling på Aarhus Universitet Ledig stilling ved Institut for Agroøkologi - Plantepatologi og Mikrobiologi, Aarhus Universitet

Professor in Epidemiology/Pathology for Agricultural Crop Plants at Aarhus University www.au.dk/om/stillinge...

Excited to have Carlos Lax @clax8.bsky.social and Ghizlane Tahiri @ghizlane-tahirizn.bsky.social recently join our lab. Give them a follow to not miss out on their fantastic science!

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Amazing new tool out by @tobybarilbio.bsky.social ! We think this is going to be a super useful tool to annotate TEs in a pangenome context!

🎉 EarlGrey ParTEA v0.1.6 is here! Huge thanks to everyone who's tried the pipeline and shared feedback — your suggestions directly shaped these new features. 🍵

#TEworldwide #transposableelements #bioinformatics #genomics

Still think this is an utterly accurate description of me. But I thought I should at least give it a try 😅

bsky.app/profile/oded...

If you're sitting on a large resequencing dataset and are dreading the pipeline work - give it a try. And if you run into issues or have feature requests, please head to the repository page.

Home – genomepanel_nf Nextflow pipeline for reference genome mapping, SNP calling and quality checks on large genome panels

Open-source, citable on Zenodo, and under active development (v1.0.5 out now).

📖 crolllab.github.io/genomepanel_nf
💻 github.com/crolllab/genomepanel_nf
🔖 doi.org/10.5281/zenodo.19392838

All processes are distributed using Nextflow & SLURM

- Downloads public data directly: just give it SRA/ENA accession numbers and it handles the rest. Obviously local fastq files work too.

- Fully containerised: Singularity images mean your results are reproducible months later, on a different cluster.

- Latest tools: GATK 4.6, bwa-mem 2.3, etc.

We've run it on plants, animals and fungi with reference genomes up to several Gb. But the design goals apply broadly:

Use compute and storage resources as efficiently as possible to speed up every stage.

Home – genomepanel_nf Nextflow pipeline for reference genome mapping, SNP calling and quality checks on large genome panels

Resequencing hundreds or thousands of individuals from the same species has become routine... but processing all those genomes efficiently? Still a headache!

Here's my solution that used to be lab-internal but that I am happy to share:

crolllab.github.io/genomepanel_...

Me after finally deciding to release some software tool and then finding bugs

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1/11 🔥 New preprint alert 🔥
We wanted to know what plants in the wild really care about. So we asked them 🎤.
Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations”
www.biorxiv.org/content/10.6...

The International Symposium on Cereal Leaf Blights isclb.com/registration in beautiful Banff from May 26-29 is approaching with a deadline for early registration/oral abstract due on March 31. @wheatinitiative.bsky.social

The latest work by @margaridasampaio.bsky.social is out as a preprint!

Using an eQTL dataset for the fungal wheat pathogen Zymoseptoria tritici, we asked whether new regulatory mutations had a predominant effect towards up- or downregulation.

Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen www.biorxiv.org/content/10.64898/2026.03...

Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen Abstract. Genomic instability caused by chromosomal rearrangements has severe consequences for organismal fitness and progression of cancerous cell lines.

Fouché, @oggenfussursula.bsky.social, McDonald & @danielcroll.bsky.social retrace chromosomal degeneration in a fungal pathogen, identifying the exact sequence triggers that initiate chromosome instability and perpetuate degenerative cycles.

🔗 doi.org/10.1093/gbe/evag037

#genome #evolution

There is an old pattern that repeats itself when someone starts gaining visibility, sooner or later the narrative shifts.

This tends to be more noticeable for people who do not come from the traditional centers of power.

The only response is to keep working, keep building, and keep moving forward.

Please share widely! We think MycoMobilome can go a long way to support high-quality TE annotations across fungi!

Also, try it on your favorite 🍄 genome and tell us what you think 😉

#TEworldwide #TEsky

MycoMobilome: a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom Abstract. Transposable elements (TEs) are found in nearly all eukaryotic genomes. Despite significant advances in the sequencing of genomes, TE resources r

Need to annotate transposons in fungal genomes? 🧬
Good news #MycoMobilome is now live! Check it out here: doi.org/10.1093/narg...
Access the sequences through our Zenodo community (you can also contribute seqs with credit), and synchronisation with @dfam.bsky.social!

w/ @danielcroll.bsky.social

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism Abstract. Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal spec

Dauphin et al. assembled a telomere-to-telomere reference genome for an ectomycorrhizal fungus with a large, repeat-rich genome, showing its genome expansion was driven by a few lineage-specific TE families in recent history.

🔗 doi.org/10.1093/gbe/evag017

#genome #evolution #TEsky

Wishing everyone a propitious start into a prosperous, successful and happy year of the horse!

Thanks for making time for the visit @edelplopez.bsky.social ! I really enjoyed the time we got to chat science. We were very excited to hear your "crazy" ideas and can't wait to see the papers coming out!

Congrats!!

Hi everyone!
The talk I had the chance to give with @fnucleosome.bsky.social last October is now out on Youtube!
If you like evolution, 3D genomics, biodiversity and/or fungi, I think you might like it! 🧬🧪🍄
The submission of this paper has never been that close!

www.youtube.com/watch?v=Plez...

Headline: "Scientists discover emperor penguin colony in Antarctica using satellite images"

Yesterday it was cows using tools, today its penguins using satellite imagery.

1/🧵
Major milestone unlocked for mycology! 🍄

We just published a massive genomic resource in 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐃𝐚𝐭𝐚, releasing 2,695 complete circular mitochondrial species assembled from public data

This single dataset nearly 𝐓𝐑𝐈𝐏𝐋𝐄𝐒 📈the known mitochondrial diversity of the Kingdom Fungi
rdcu.be/eYZ2h