Daniel Croll
@danielcroll.bsky.social
We want to understand how pathogens adapt and cause diseases. Also passionate about TEs, pangenomes & population genomics, bioinformatics and conservation genomics.
Professor of Evolutionary Genetics @ University of Neuchatel 🇨🇭
Hobbies: 👧🏻👧🏼🏔️🏕️
Professor of Evolutionary Genetics @ University of Neuchatel 🇨🇭
Hobbies: 👧🏻👧🏼🏔️🏕️
Pinned
Daniel Croll
@danielcroll.bsky.social
· Nov 12
Big congratulations @tobybarilbio.bsky.social!
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Reposted by Daniel Croll
Earlier this week, David Marques, my beloved PhD brother, died after a battle with cancer. He was an amazing person, friend, father, husband, scientist, collaborator, birder, among other things. I am immensely grateful for many years of friendship and close collaboration with him. We miss you!
January 10, 2026 at 9:14 AM
Earlier this week, David Marques, my beloved PhD brother, died after a battle with cancer. He was an amazing person, friend, father, husband, scientist, collaborator, birder, among other things. I am immensely grateful for many years of friendship and close collaboration with him. We miss you!
Reposted by Daniel Croll
Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti...
Thanks to those who already shared the link!
Thanks to those who already shared the link!
Blinded by the lights? Re-examining the adaptive role of transposable elements in plants with population genomics
Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype…
www.sciencedirect.com
January 5, 2026 at 9:02 AM
Have we been overstating the role of transposable elements in adaptation to local or rapidly changing environmental conditions? Happy to share my (somewhat unpopular?) opinion paper on this matter: www.sciencedirect.com/science/arti...
Thanks to those who already shared the link!
Thanks to those who already shared the link!
Reposted by Daniel Croll
Depends on the pathogen, I guess. However, generally, if the effector mutation that led to overcoming the R gene does not lead to a fitness or virulence penalty for the pathogen, that mutated allele wil be kept, and thus the R gene will not be "forgotten".
January 7, 2026 at 1:07 PM
Depends on the pathogen, I guess. However, generally, if the effector mutation that led to overcoming the R gene does not lead to a fitness or virulence penalty for the pathogen, that mutated allele wil be kept, and thus the R gene will not be "forgotten".
Welcome to Bluesky Leila @leilaebrahimi.bsky.social!
December 28, 2025 at 9:51 AM
Welcome to Bluesky Leila @leilaebrahimi.bsky.social!
Reposted by Daniel Croll
Alkemade, @timbarra.bsky.social et al. did temporal association analysis on three major fungal crop pathogens collected between 1956 and 2023, identifying genes linked to fungicide resistance and stress responses as frequent sites of adaptation.
🔗 doi.org/10.1093/gbe/evaf241
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf241
#genome #evolution
Genomic Insights into Historical Adaptation of Three Key Fungal Plant Pathogens
Abstract. Fungal culture collections hold a wealth of historical isolates that could be used to study fungal evolution over the past decades, an era that c
doi.org
December 23, 2025 at 9:11 AM
Alkemade, @timbarra.bsky.social et al. did temporal association analysis on three major fungal crop pathogens collected between 1956 and 2023, identifying genes linked to fungicide resistance and stress responses as frequent sites of adaptation.
🔗 doi.org/10.1093/gbe/evaf241
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf241
#genome #evolution
Reposted by Daniel Croll
Benjamin Adjei
Croll lab at University of Neuchatel. PhD student
pathogen-genomics.org
December 10, 2025 at 9:17 PM
Reposted by Daniel Croll
Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social
www.cell.com/current-biol...
www.cell.com/current-biol...
December 9, 2025 at 5:20 PM
Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by Daniel Croll
Thrilled to be hosting this session with @henriklicht.bsky.social and @agesiorska.bsky.social 🥳
Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! 🤩
Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! 🤩
Organisers
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen
Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen
Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel
December 5, 2025 at 8:42 AM
Thrilled to be hosting this session with @henriklicht.bsky.social and @agesiorska.bsky.social 🥳
Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! 🤩
Already looking forward to @danielcroll.bsky.social's talk and the other talks and posters that'll form part of this session! 🤩
Reposted by Daniel Croll
Organisers
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen
Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen
Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel
December 3, 2025 at 5:47 PM
Organisers
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen
Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel
- Henrik H. de Fine Licht | University of Copenhagen
- @drandiwilson.bsky.social | University of Copenhagen
- @agesiorska.bsky.social | University of Copenhagen
Invited Speaker
- @danielcroll.bsky.social | University of Neuchatel
Big congratulations @guidopuccetti.bsky.social !! Very proud of your achievement.
It can feel like an eternity as a PhD student sometimes to see their first chapter in published form. Enjoy the moment!! 🎉
It can feel like an eternity as a PhD student sometimes to see their first chapter in published form. Enjoy the moment!! 🎉
Finally out!
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...
A big thanks to @danielcroll.bsky.social & @GabrielScalliet
#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...
A big thanks to @danielcroll.bsky.social & @GabrielScalliet
#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen | mBio
Sustainable food production requires the management of disease agents attacking crops.
Application of antifungal compounds is among the key elements of pathogen containment;
however, resistance can ri...
journals.asm.org
December 1, 2025 at 12:58 PM
Big congratulations @guidopuccetti.bsky.social !! Very proud of your achievement.
It can feel like an eternity as a PhD student sometimes to see their first chapter in published form. Enjoy the moment!! 🎉
It can feel like an eternity as a PhD student sometimes to see their first chapter in published form. Enjoy the moment!! 🎉
Reposted by Daniel Croll
Finally out!
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...
A big thanks to @danielcroll.bsky.social & @GabrielScalliet
#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...
A big thanks to @danielcroll.bsky.social & @GabrielScalliet
#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen | mBio
Sustainable food production requires the management of disease agents attacking crops.
Application of antifungal compounds is among the key elements of pathogen containment;
however, resistance can ri...
journals.asm.org
December 1, 2025 at 12:00 AM
Finally out!
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...
A big thanks to @danielcroll.bsky.social & @GabrielScalliet
#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen
journals.asm.org/doi/10.1128/...
A big thanks to @danielcroll.bsky.social & @GabrielScalliet
#azole #DMI #GWAS #fungicide #resistance #zymoseptoria #Europe
Reposted by Daniel Croll
Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen - BMC Biology
Background Genome spatial organization plays a fundamental role in biological function across all domains of life. While the principles of nuclear architecture have been well-characterized in animals ...
link.springer.com
November 28, 2025 at 12:43 PM
Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Reposted by Daniel Croll
Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
November 18, 2025 at 8:41 AM
Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Reposted by Daniel Croll
The number of Project funding applications and the requested amounts have risen to record levels, consequently decreasing researchers' chances of receiving a grant.📈⚠️
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
New record in Project funding
SNSF Project funding reaches an all-time high with 1,451 applications and CHF 1.3 billion requested – while federal funding is stagnating.
buff.ly
November 24, 2025 at 8:30 AM
The number of Project funding applications and the requested amounts have risen to record levels, consequently decreasing researchers' chances of receiving a grant.📈⚠️
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
Evaluation is under way, and funding decisions will follow in spring 2026.
➡️ buff.ly/gEdD3OY
#research #science
Reposted by Daniel Croll
Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....
Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology®
Pathogens’ responses to sudden temperature fluctuations, spanning various temporal scales, are critical determinants of their survival, growth, reproduction, and homeostasis. Here, we combined phenoty...
apsjournals.apsnet.org
November 21, 2025 at 1:00 PM
Responses to Temperature Shocks in Zymoseptoria tritici Reveal Specific Transcriptional Reprogramming and Novel Candidate Genes for Thermal Adaptation | Phytopathology® apsjournals.apsnet.org/doi/full/10....
Reposted by Daniel Croll
Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis
### Competing Interest Statement
The authors have declared no competing interest.
Agriculture and Agri-Food Canada, https://ror.org/051dzs374
Alberta Grain
Saskatchewan Wheat Development Commissio...
www.biorxiv.org
November 18, 2025 at 4:22 PM
Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
On my way to visit the very impressive CAS Institute of Microbiology in Beijing. Then, on to the AMC in Guangzhou.
Very excited about my first trip to China.
Very excited about my first trip to China.
November 18, 2025 at 3:48 PM
On my way to visit the very impressive CAS Institute of Microbiology in Beijing. Then, on to the AMC in Guangzhou.
Very excited about my first trip to China.
Very excited about my first trip to China.
Big congratulations @tobybarilbio.bsky.social!
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
November 12, 2025 at 3:38 PM
Big congratulations @tobybarilbio.bsky.social!
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Please check out and share our final version of the transposon mobilization work in a fungal pathogen - out now in Nature Communications
www.nature.com/articles/s41...
Reposted by Daniel Croll
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...
www.nature.com
November 12, 2025 at 1:17 PM
TEs aren’t just genomic parasites, they’re also engines of genomic novelty.
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion.
With @danielcroll.bsky.social & @guidopuccetti.bsky.social
🧬 www.nature.com/articles/s41...
#TEworldwide
Reposted by Daniel Croll
My new Emmy Noether Group is recruiting!
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
Aktuelle Ausschreibungen
Aktuelle Ausschreibungen
www.uni-kiel.de
November 3, 2025 at 9:03 AM
My new Emmy Noether Group is recruiting!
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
🔬 Two PhD positions in plant pathogen evolution
🧬 Start: April 2026 (flexible)
📍 Dept. of Phytopathology & Plant Protection @rstam.bsky.social @uni-kiel.de
⏰ Apply by 15 Dec 2025
🔗 More info: www.uni-kiel.de/personal/de/...
Do get in touch or share 😊
Reposted by Daniel Croll
Still using 16S/ITS profiling? You might want to reconsider👀
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome
Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...
microbiomejournal.biomedcentral.com
October 30, 2025 at 1:32 PM
Still using 16S/ITS profiling? You might want to reconsider👀
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....
Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....