Gautam Shirsekar
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coevolution.bsky.social
Gautam Shirsekar
@coevolution.bsky.social
78 followers 68 following 26 posts
Plant pathologist | Genomics | Coevolution | Wild plant pathosystems | Weigelworld, Max Planck Institute for Biology | Asst. Prof. at the University of Tennessee, Knoxville (EPP)| www.coevolutionlab.org
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coevolution.bsky.social
Gautam Shirsekar @coevolution.bsky.social · Aug 14
~ 5 and 1/2 years ago, my then postdoc advisor @plantevolution.bsky.social gave me complete freedom to assemble a team and interrogate NLR diversity in pangenomic context. We used @pacbio.bsky.social CCS and Iso-Seq, to annotate genomes with pathogen-challenged transcriptome. We then manually.....
Reposted by Gautam Shirsekar
natplants.nature.com
New Correspondence: "Rethinking the need for field trials" rdcu.be/eM96P
October 28, 2025 at 7:12 PM
Reposted by Gautam Shirsekar
plantevolution.bsky.social
2/2 Our lab pioneered the use of genome graphs already 16 years ago! Read this oldie-but-goldie from @labschneeberger.bsky.social and Jörg Hagmann: Simultaneous alignment of short reads against multiple genomes
genomebiology.biomedcentral.com/articles/10....
October 27, 2025 at 5:53 PM
Reposted by Gautam Shirsekar
plantevolution.bsky.social
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...
October 27, 2025 at 5:53 PM
coevolution.bsky.social
October 27, 2025 at 1:01 PM
coevolution.bsky.social
@annaliisalaine.bsky.social
Does this look familiar to you? From Cherokee National Forest
September 16, 2025 at 3:58 PM
Reposted by Gautam Shirsekar
plantevolution.bsky.social
Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...
August 20, 2025 at 6:23 AM
Reposted by Gautam Shirsekar
cp-cellhostmicrobe.bsky.social
Plant NLR evolution
Annotated, divergent A. thaliana genomes &pangenome graph approaches describe genomic neighborhoods of NLRs, revealing evolutionary footprints in form of “diversity in diversity” at these loci
Weigel @mpi-bio-fml.bsky.social @coevolution.bsky.social‬
www.cell.com/cell-host-mi...
Pangenomic context reveals the extent of intraspecific plant NLR evolution
Individual- and population-level diversity is required for pathogen defense by nucleotide-binding site leucine-rich repeat (NLR) proteins. Teasdale et al. leverage annotated, divergent A. thaliana gen...
www.cell.com
August 15, 2025 at 3:08 PM
coevolution.bsky.social
~ 5 and 1/2 years ago, my then postdoc advisor @plantevolution.bsky.social gave me complete freedom to assemble a team and interrogate NLR diversity in pangenomic context. We used @pacbio.bsky.social CCS and Iso-Seq, to annotate genomes with pathogen-challenged transcriptome. We then manually.....
August 14, 2025 at 9:13 PM
Reposted by Gautam Shirsekar
plantevolution.bsky.social
Out after peer review now, follow up from our 2019 pna-NLRome paper (which was based on enrichment and long-read sequencing). It is remarkable how much more can be learned with complete genome sequences. Next. pan-NLRome from hundreds of A. thaliana long-read genomes! Big thanks to the entire team!
August 14, 2025 at 1:42 PM
Reposted by Gautam Shirsekar
plantevolution.bsky.social
1/2 What's best: a field-first or lab-first approach? No easy answers but differences between lab and field should not be seen as failure but motivate further inquiry and allow complementary discovery. Read our thoughts on this here:
www.sciencedirect.com/science/arti...
Lab to field: Challenges and opportunities for plant biology
Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between l…
www.sciencedirect.com
August 14, 2025 at 3:44 PM
Reposted by Gautam Shirsekar
kdm9.bsky.social
Feel free to ask any q's here
August 14, 2025 at 5:55 AM
Reposted by Gautam Shirsekar
kdm9.bsky.social
We show that pangenome graphs provide a flexible way to define the context within which NLR evolution occurs, and that graph metrics capture diversity in both sequence and structure, and show that such diversity is centered on NLRs themselves
The neighborhood containing RPP4/RPP5 is among the most complex, and the highly elevated local complexity is focused on NLR genes and pseudogenes. Each per-accession track consists of both a trace of local pangenomic complexity (above the abscissae), and a representation of the gene annotation (below the abscissae). Individuals show extreme haplotypic diversity of NLRs, which is reflected in highly elevated local complexity focused on NLR genes and their immediate surrounds, while TE genes or other protein-coding genes show little elevation in complexity above the genome background. For an enlarged version contrasting two nearby neighborhoods, please see Figure S3.
August 14, 2025 at 5:55 AM
Reposted by Gautam Shirsekar
kdm9.bsky.social
Long story short: we assemble 17 representative Arabidopsis thaliana genomes, exhaustively annotate NLRs with long read evidence & manual curation, and assay many measures of NLR diversity.
(A and B) Our 17 accessions (squares) are broadly representative of both the geographic and population genetic distributions of the broader 1,001 Genomes collection (circles23); inset shows the UMAP embedding of 17 accessions in the co-ancestry space of all 1,135 accessions (adapted from Shirsekar et al.21). Colors in (A) and (B) represent the haplotype sharing groups from Shirsekar et al.21; samples in gray represent the three haplotype sharing groups not represented by our 17 accessions and their corresponding selected accession (see E). (C) Phenotypic diversity of 17 accessions (rows) with respect to the oomycete pathogen Hyaloperonospora arabidopsidis (Har; columns), with resistant phenotypes denoted as black. 104 Har accessions were collected across Europe, as described in STAR Methods. (D) Universal, pangenome-wide syntenic anchors define NLR neighborhoods. (E) Representative example of an NLR neighborhood, highlighting accurate delineation of the borders of NLR-containing variable regions, regardless of structural or presence/absence variation. Black bars indicate pangenomic neighborhoods, syntenic anchors in pink. A fixed-sized window approach centered on a focal NLR (in yellow) would produce a very different outcome. Note accession codes used in this paper of the form atNNNN represent Arabidopsis ecotype IDs, see Alonso-Blanco et al.23 and Table S1.
August 14, 2025 at 5:55 AM
coevolution.bsky.social
'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory
August 14, 2025 at 8:22 PM
coevolution.bsky.social
Come join EEB at the University of Tennessee at Knoxville.

Evolutionary Genomics, Assistant Professor, Ecology & Evolutionary Biology, Fall 2026
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functional and evolutionary genomics in any system 🌱, 🦠, or 🦌 (including 👫)
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July 28, 2025 at 5:46 PM
coevolution.bsky.social
I am Grape!
May 14, 2025 at 7:55 PM
coevolution.bsky.social
#MemPanG25
@thinks.lol
May 12, 2025 at 10:08 PM
coevolution.bsky.social
In the Smokies, on a wild grape hunt
May 5, 2025 at 1:04 AM
coevolution.bsky.social
1/6 Today is Labor Day in USA and we decided to release the results of our labor and rigor on NLR evolution as a preprint. www.biorxiv.org/content/10.1...
Pangenomic context reveals the extent of intraspecific plant NLR evolution
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
September 2, 2024 at 10:08 PM
coevolution.bsky.social
Wild Flower Festival, Frozen Head State Park, #TN #statepark
#TNPS, Tennessee Native Plant Society #naturalist
April 15, 2024 at 12:48 AM
coevolution.bsky.social
Wild Flower Festival, Frozen Head State Park, #TN #statepark
#TNPS, Tennessee Native Plant Society #naturalist
April 15, 2024 at 12:47 AM
coevolution.bsky.social
Wild Flower Festival, Frozen Head State Park, #TN #statepark
#TNPS, Tennessee Native Plant Society #naturalist
April 15, 2024 at 12:46 AM