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Today is Labor Day in USA and we decided to release the results of our labor and rigor on NLR evolution as a preprint. Pangenomic context reveals the extent of intraspecific plant NLR evolution.
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Gautam Shirsekar
865 posts
Gautam Shirsekar
@gaushi
Plant pathologist | Genomics | Coevolution | Wild plant pathosystems | Weigelworld, Max Planck Institute for Biology | Asst. Prof. at the University of Tennesse
Knoxville, TN, USA Katılım Şubat 2009
443 Takip Edilen335 Takipçiler
Gautam Shirsekar retweetledi
Congratulations to Anugya Bhattarai on receiving the 2025 Steven C. Nelson Early Career Development Fellowship from @plantdisease. With support from APS, Anugya will visit study how robotic tools and deep learning can help identify wild grapes resistant to downy mildew. #epptn
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Gautam Shirsekar retweetledi
Recent @UT_Herbert graduate Rachel Carpenter used her HERO internship to gain hands-on experience. She now works as a research technician for the CoEvolution Lab, where she channels her lifelong passion for science. #epptn @UTIAg @UTKnoxville
Learn More: epp.tennessee.edu/building-a-car…
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@ESPM_Berkeley @UCBerkeley @alexzebra321 @MonicaDonegan3 Amazing work!! Congratulations @alexzebra321
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Gautam Shirsekar retweetledi
Researchers from the @UCBerkeley lab of Professor Rodrigo Almeida used bacterial DNA from a 120-year-old herbarium specimen to reconstruct the history of how Pierce’s disease—which causes more than $100 million in losses a year—spread across California. news.berkeley.edu/2024/12/16/wha…
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Gautam Shirsekar retweetledi
How did I miss this one rb.gy/7t7wwf maybe is time to reconsider talking about Growth-defense trade-offs and start considering changes in growth and life history traits as part of defense mechanisms. Our results rb.gy/qyt30u and rb.gy/4huf3e
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Gautam Shirsekar retweetledi
Our latest research on position-dependent transcriptional regulatory sequences in plants is now published! 🌿 More details in our preprint tweet and in this thread! 👇
nature.com/articles/s4158… 📄🔍
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Yoav Voichek (plant-trx.bsky.social)@voichek
Transcription regulation in plants vs. animals - same-same or different? We show in a new preprint that in plants, regulatory sequences next to the TSS are position-dependent - as opposed to animal enhancers which are position-independent (1/6) biorxiv.org/content/10.110…
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Gautam Shirsekar retweetledi
“Direct from Nature” brought together an #ecologist, Dana Warren, #forest #pathologist, David Shaw, and #art #historian, Harper Loeb-great presentation focusing on how 19th century landscape paintings can provide insights into environmental changes in eastern forests.
McClung Museum@McClungMuseum
Starting at 5:30 pm! Join us for a free lecture exploring the intersections of art and science: tiny.utk.edu/directfromnatu…
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Gautam Shirsekar retweetledi
The Budke Lab @UTK_EEB is recruiting #PhD students to start fall 2025. Applications due Dec 1. Check out our lab website to see if your research interests are a good fit jmbudke.github.io & then reach out via email. Please RT & thanks! #gradschool #phdjourney
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Gautam Shirsekar retweetledi
This is a great resource! I use some of these as examples of how to write a beautifully crafted proposal in my writing class.
Jeffrey Ross-Ibarra@jrossibarra
If you’ve gotten an NSF PRFB and want to pay it forward please consider sharing yours publicly on my GitHub!
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Gautam Shirsekar retweetledi
Evolution in overdrive of plant immune receptors - population level view
👍🌱🌱🌱
Gautam Shirsekar@gaushi
We constructed a pangenome graph with #pggb @erikgarrison to crawl along the regions of the genomes where NLRs or pieces of NLRs are found at least in 1 accession UNTIL we found common (syntenic) anchors bordering those regions in all the accessions --> "NLR neighborhood"
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Gautam Shirsekar retweetledi
Do we have to choose between chocolate and biodiversity? @UTIAg researchers received a $120,000 grant from @USDA_NIFA to find out. Led by graduate student Holly Brabazon, the team is studying wild cacao trees in Belize to promote sustainable farming.#epptn tiny.utk.edu/utia-researche…
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Gautam Shirsekar retweetledi
Greatly recommended!, amazing supervisor, exciting science and ensured fun. What are you waiting to apply??!!!
Beth Rowan@random_roll
Come join me as a research assistant and have fun working on genome editing and plant tissue culture projects! jobs.oregonstate.edu/postings/159131
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@ADSteinbrenner and that ADR2 diversification is contained within a neighborhood by different processes
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Interesting new analysis of NLR pangenome variation.
I like the simple approach for defining sub-orthogroups, termed "OG70s", by CD-HIT >70% similarity. For example six OG70 subclades of the ADR2 OG are shown in Fig 5B.
"fewer than 18% of OG70s are present in all accessions."
Gautam Shirsekar@gaushi
We assembled 17 diverse *A. thaliana* (Ath) genomes using @PacBio #CCS and annotated them using @PacBio #isoseq reads that were obtained by challenging these accessions with three different Hyaloperonospora arabidopsidis (Har) strains.
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Gautam Shirsekar retweetledi
How do you quantify the natural variation of plant immunity?
Thrilled to announce the preprint publication of our superb collaboration effort led by @gaushi, @PlantEvolution, Luisa Teasdale, and Kevin Murray on inferring NLR biodiversity across natural Arabidopsis accessions. 🌱
Gautam Shirsekar@gaushi
We constructed a pangenome graph with #pggb @erikgarrison to crawl along the regions of the genomes where NLRs or pieces of NLRs are found at least in 1 accession UNTIL we found common (syntenic) anchors bordering those regions in all the accessions --> "NLR neighborhood"
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Today is Labor Day in USA and we decided to release the results of our labor and rigor on NLR evolution as a preprint. Pangenomic context reveals the extent of intraspecific plant NLR evolution.
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@Rootstrapping Close to the East Coast in Bioinfo apply.interfolio.com/149845
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Are you intrigued? Here is our work by Luisa, Kevin, Max, @aconga7, Theresa, Leon, Justina, Christa, Oliver, Joffrey, Regina, Rosanne, @HajkDrost @PlantEvolution biorxiv.org/content/10.110…
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Neighborhoods "expand" & "contract" in accessions and offer a richer picture of NLR evolution in (genomic) space and (evolutionary) time. Why does it matter? Because, NLRs didn't just fell out of a 🌴, they exist in the context of all in which they live and what came before them
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