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Reposted by Gautam Shirsekar

Nature Plants @natplants.nature.com · 28/10/2025

New Correspondence: "Rethinking the need for field trials" rdcu.be/eM96P

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Reposted by Gautam Shirsekar

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/10/2025

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....

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Reposted by Gautam Shirsekar

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/10/2025

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...

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Gautam Shirsekar @coevolution.bsky.social · 16/09/2025

@annaliisalaine.bsky.social Does this look familiar to you? From Cherokee National Forest

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Reposted by Gautam Shirsekar

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 20/08/2025

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...

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Reposted by Gautam Shirsekar

Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 15/08/2025

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...

cell.com

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...

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Gautam Shirsekar @coevolution.bsky.social · 14/08/2025

..... these alleles have arrived there following many ways and will continue their evolutionary journey in natural pathosystems. This research was intellectually stimulating and rewarding experience for all of us. Check it out in @cp-cellhostmicrobe.bsky.social latest issue........

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Gautam Shirsekar @coevolution.bsky.social · 14/08/2025

.....through transposable elements along the way. 'hoods allowed us to look beyond traditional definitions of NLR clusters and their patterns of evolution. Context made us realize that NLRs are remarkable in their diversity even more than previously thought. When we study NLRs in the lab....

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Gautam Shirsekar @coevolution.bsky.social · 14/08/2025

.....curated the NLRs with help of a computational pipeline. Meanwhile, the development of PGGB @thinks.lol and ODGI @andreaguarracino.bsky.social made us wander into the land of graphs and use network theory to propose concept of "pangenomic NLR neighborhoods". We also navigated.....

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Gautam Shirsekar @coevolution.bsky.social · 14/08/2025

~ 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.....

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Reposted by Gautam Shirsekar

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/08/2025

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!

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Reposted by Gautam Shirsekar

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 14/08/2025

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...

sciencedirect.com

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…

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Reposted by Gautam Shirsekar

K.D. Murray @kdm9.bsky.social · 14/08/2025

Feel free to ask any q's here

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Reposted by Gautam Shirsekar

K.D. Murray @kdm9.bsky.social · 14/08/2025

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.

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Reposted by Gautam Shirsekar

K.D. Murray @kdm9.bsky.social · 14/08/2025

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.

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Gautam Shirsekar @coevolution.bsky.social · 14/08/2025

'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

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Gautam Shirsekar @coevolution.bsky.social · 28/07/2025

Come join EEB at the University of Tennessee at Knoxville. Evolutionary Genomics, Assistant Professor, Ecology & Evolutionary Biology, Fall 2026 apply.interfolio.com/170735 functional and evolutionary genomics in any system 🌱, 🦠, or 🦌 (including 👫)

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Gautam Shirsekar @coevolution.bsky.social · 05/05/2025

In the Smokies, on a wild grape hunt

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Gautam Shirsekar @coevolution.bsky.social · 02/09/2024

5/6 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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Gautam Shirsekar @coevolution.bsky.social · 02/09/2024

4/6 We constructed a pangenome graph with #pggb @erikg.bsky.social 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 @coevolution.bsky.social · 02/09/2024

3/6 With a rigorous annotation that involved manual curation and semi-automated decision-making algorithm we pinned down every single NLR (genes, pseudogenes, "protopseudogenes") and even remnants of NLRs.

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Gautam Shirsekar @coevolution.bsky.social · 02/09/2024

2/6 We assembled 17 diverse *A. thaliana* (Ath) genomes using @pacbio.bsky.social #CCS and annotated them using #isoseq reads that were obtained by challenging these accessions with three different Hyaloperonospora arabidopsidis (Har) strains.