K.D. Murray
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kdm9.bsky.social
K.D. Murray
@kdm9.bsky.social
290 followers 850 following 17 posts
A scientist, mostly

Naarm/Melbourne, AU & Tübingen, DE
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kdm9.bsky.social
We also highlight the importance of using multiple independent measures of NLR diversity, including expression, structural, sequence, and domain diversity, as each tells a different story of NLR diversification.
(A) Variation of OG70 diversity across different axes. If not stated otherwise, always for all OG70 members across all accessions (A). π, mean nucleotide pairwise distance; entropy, mean Shannon entropy of column states within an amino acid multiple sequence alignment, excluding positions with fewer than 10 non-gap characters; local complexity, mean pangenome local complexity; severe mutations, sum of allele frequencies of mutations with severe predicted consequences among the 1,001 Genomes collection for OG70s present in at9852; copies, mean number of copies per accession; domains, mean Simpson’s index of diversity of NLR-associated domains detected by NLRtracker; isoforms, mean of Simpson’s index of diversity of isoform variation affecting the open reading frame of each transcript; gene-body methylation, mean percentage of methylated CpG sites. Enlarged in Figure S4, and Figures S5–S8 explore each individual axis in more detail.
August 14, 2025 at 5:55 AM
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
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
kdm9.bsky.social
Out today in Gigascience: Exploring the role of polymorphic inter-species structural variants in reproductive isolation and adaptive divergence in Eucalyptus
academic.oup.com/gigascience/...
#eucalyptus #genomics #speciation #structuralvariants #evolution
Figure one from the paper, showing the different types of structural variation found between species
June 14, 2024 at 6:37 AM