Scheme that summarizes the workflow for the identification of non-autonomous TEs
🛠️ Overall, we illustrate some of the blind spots in the current TE annotation pipelines and propose strategies for better detection of non-autonomous LTR retrotransposons (TRIMs).
🔎 Let’s learn more about genomes together!
📚 www.biorxiv.org/content/10.6...
Sequence features of non-autonomous LTR retrotransposons
Presence/Absence of target site duplications of all non-autonomous LTR retrotransposon families -- this indicates the degree of genuine insertions vs. recombination-derived TEs
There is a deep dive into sequence details and looking into the kond of insertions that non-autonomus TEs produce.
Takeaway:
- non-autonomous LTR retrotransposon diversity is vastly underestimated
- they recombine heavily
- partnerships with autonomous TEs are often not similarity based
Length distribution of non-autonomous LTR retrotransposons
Our lab member Sophie deep-dived into the genome of one of the plants we know best (sugar beet).
She identified over 100 non-autonomous LTR retrotransposon families hiding in the genome. Many elements are rather long (length distribution ⬇️), often without any sequence similarity to coding TEs.
Scheme of a non-autonomous LTR retrotransposon
Some insights into the identification process / pearameter runs to identify non-autonomous LTR retrotransposons
Non-autonomous LTR retrotransposons (often named TRIMs) can give you headache -- they don't encode anything!
So how can you even identify them?
Well, with a lot of structure-based identification runs and a lot of manual verification (some insight ⬇️).
🧬🔎 Deep dive into plant #TransposableElements
❓ If you identify all autonomous #TEs, you will automatically also have all non-coding derivates, right? Right?
Well, no! Not even close. Check out here, how much you are missing:
📚 www.biorxiv.org/content/10.6...
#TEsky
Haha, hallo Sarah, was für eine Überraschung! Machen wir! Ich bin jetzt seit etwas über einem Jahr in Aachen und wir können uns gern treffen! Ich würde mich sehr darüber freuen!
Thank you for looking this up. Also, I had not remembered that the Llorens paper had time estimates.
Our paper is now out in Nature:
“Ancient co-option of LTR retrotransposons as yeast centromeres”
www.nature.com/articles/s41...
A short thread on how retrotransposons helped give rise to yeast point centromeres.
1/14
Anyone knows, how this was this calculated? Maybe gene distance of BUSCOs vs. gene distance of the gagpol?
Mitosis has a timing system. If chromosomes attach properly, cells divide on schedule and keep proliferating. If attachment is slow or incomplete, the delay is recorded — and daughter cells stop dividing.
We explore this link in our new preprint.
🔗 www.biorxiv.org/content/10.6...
1/3 Jellyfish and anemones also sleep, despite not having a brain
Not only do they sleep, but their behavior is affected if they lack sleep; they become clumsier and need to catch up on lost sleep. Interestingly, they sleep 8 hours a day, just like us.
(paper) www.nature.com/articles/s41...
Extensive horizontal transfer of transposable elements shapes fungal mobilomes
@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social
www.cell.com/current-biol...
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis | Science www.science.org/doi/10.1126/...
Very nice work from Holger Puchta & colleagues
NEW Publication🥳
Rapid #evolution is thought to be disadvantageous due to the accumulation of deleterious #mutations. We identify multiple lineages of rapidly evolving and stable #yeast that are many millions of years old
🔗: academic.oup.com/mbe/advance-...
Job posting: berufungsportal.rwth-aachen.de?showProcedur...
Application portal:
www.berufungsportal.rwth-aachen.de
Please call me, if you need more information.
4/4
🌏 Aachen is a beautiful and historic "student city" in a very central European location, directly where Germany, Belgium, and the Netherlands connect.
one-million-places.com/en/germany/a...
3/4
🌏Where? Germany, RWTH Aachen University
@rwth.bsky.social
👍The RWTH is the second largest technical university in Germany and scores high in international rankings.
🌱 Plants at RWTH: www.biologie.rwth-aachen.de/cms/biologie...
2/4
Job posting. We look for a Full Professor (W3) of Stress Resilience of Plants at the RWTH Aachen.
We are looking for a colleague to join us at RWTH Aachen University:
🌱 Full Professor in Stress Resilience of Plants (W3 tenured)
📌What are we looking for? Someone working with us strategically at the interface of plant biology/ physiology/ resilience
#academicjobs #facultyjobs #PlantJobs
1/4
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
How does life evolve to adapt to modern cities?
Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.
🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Roles of No-Go RNA decay in the control of plant viruses and transposable elements
->BMC Plant Biology | More from Lil' Dr Glen EcoChat at BigEarthData.ai
fun seeing these haplotypes being resolved
also: shortbread, short read, or both? (and as i love shortbread: is there a shortbread recipe using corn instead of wheat?)
This work was led by @jiangzhaoqian.bsky.social, who is dedicated to make your life in genomics and #TransposableElement curation a lot easier. We are very happy to have him now in our group and that we could help with his vision.
Try TEtrimmer: github.com/qjiangzhao/T...
New Software Simplifies Analysis of “Jumping Genes”
Ralph Panstruga, @toheitka.bsky.social, and Lisa Fürtauer from @rwth.bsky.social
in @natcomms.nature.com (DOI: 10.1038/s41467-025-63889-y)
www.rwth-aachen.de/cms/root/wir...
I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...
Collaborative work between Durbin Lab at Cambridge & Svardal Lab at Antwerp 🐠
🔗 to manuscript: www.science.org/doi/10.1126/...
Our recent article on transposable elements and aging - which made the June cover - is the focus of a new Highlight.
"Highlight: 'Jumping Genes' Caught in an Aging Merry-Go-Round"
🔗 doi.org/10.1093/gbe/evaf094
🖌️ Miriam Merenciano
#genome #TEsky
Super excited to release a huge evolution project on the works for many years:
Evolution experiments synchronized across climates to understand rapid adaptation
Preprint: doi.org/10.1101/2025...
All data available: www.grene-net.org/data
#MOILAB
@ucberkeleyofficial.bsky.social
@hhmi.org
🧵👇
Love HMMER.
Like many recent decisions, this is incredibly short-sighted. I fail to see how being recognized globally to produce excellent work is of no use to the country.
Greetings from Europe.
🌱 We will soon open the search for a new W3 Professor in Plant Stress Resilience / Molecular Plant Physiology.
🌏Where? Germany, RWTH Aachen University @rwth.bsky.social
We plan to look widely. Please let me know, if you want to be updated on the job announcement.
#AcademicJobs
