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Gautam Shirsekar

@coevolution.bsky.social

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

26 Posts90 Follower73 Folgt
Cell Host & Microbe@cp-cellhostmicrobe.bsky.social · 12mo ago

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...

cell.com

PlantEvolution 🌱🌾@plantevolution.bsky.social · 12mo ago

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!

K.D. Murray@kdm9.bsky.social · 12mo ago

Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution" www.cell.com/cell-host-mi... #plantscience #plantimmunity #pangenomes #science #nlr

PlantEvolution 🌱🌾@plantevolution.bsky.social · 12mo ago

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…

sciencedirect.com

K.D. Murray@kdm9.bsky.social · 12mo ago

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.
K.D. Murray@kdm9.bsky.social · 12mo ago

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.
Gautam Shirsekar@coevolution.bsky.social · 12mo ago

'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

K.D. Murray@kdm9.bsky.social · 12mo ago

Happy to be able to finally share our NLR pangenome paper, out now in CHM. "Pangenomic context reveals the extent of intraspecific plant NLR evolution" www.cell.com/cell-host-mi... #plantscience #plantimmunity #pangenomes #science #nlr