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S. Lorena Ament @loreament.bsky.social · 07/08/2026

Finally, we went a bit crazy and looked for HIC NLRs all across the tree of life. Different kinds of proteins can have HIC repeats, but we found that they often have an NLR configuration. Could HIC be advantageous in the context of self-nonself recognition in other taxa too? 10/n

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

We also confirmed that HIC NLR paralogs exchange repeat units from the Cterm, increasing allelic diversity and fast evolution. This process potentially makes them sources of genetic load too, as observed in a few well-studied allorecognition NLRs that cause reproductive incompatibilities. 9/n

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

We also aimed at distinguishing balancing selection from #introgression, by contrasting patterns of differentiation, trans-species polymorphism, and by examining signatures of selective sweeps. It turns out that NLRs are preferentially introgressed between species! 8/n #hybridization

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

HIC NLRs are more associated with transposable elements, have a higher mutational input (probably from a process called RIP), higher piN/piS, higher dN/dS, higher Tajima's D, you name it. They are funky! 7/n #popgen #molecularevolution #transposons

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

We reasoned that if NLRs have a general immune function, we should observe signals in their molecular evolution, such as fast gene turnover, gene expansions and balancing selection. And that's exactly what we found! HIC NLRs are particularly crazy! 6/n #popgen #balancingselection

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

NLR genes, although constructed somewhat differently, exist in other domains of life. NLRs are key components of the innate immune system in plants, animals and even bacteria. So what if fungal NLRs are also generally defense genes, rather than just #allorecognition genes? 4/n

Illustration of fungal hyphae encountering bacteria as a possible pathogen (by S. Lorena Ament-V.)

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

Podosporologists have been studying vegetative fusion between different individuals (allorecognition) since the 50s! So we know there are 9 allorecognition genes in P. anserina, and 4 of those are NLRs. But there are >60 other NLR genes in #Podospora genomes. What are those doing? 3/n

Two Podospora strains growing side by side and showing a rejection reaction to fusion when meeting at the growing front (allorecognition)

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S. Lorena Ament @loreament.bsky.social · 07/08/2026

Previous studies took more of a macroevolutionary perspective, or did not look at NLRs specifically. So we focused on #Podospora anserina and its relatives, model systems for studying the molecular mechanisms of self/nonself recognition. 2/n

A fruiting body of Podospora with "Thug Life" cartoon sunglasses.

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S. Lorena Ament @loreament.bsky.social · 07/07/2026

Me trying to run minigraph-cactus to be like the cool pangenome kids #Pangenome #genomics

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

For the repeat domain, we extracted >1100 individual repeats and performed a PCA of their nucleotide sequences. Indeed, het-d and het-e are not that similar, but we discovered that het-e seems to be exchanging repeats with another gene! 8/n

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

Are het-d and het-e capable of recognizing het-c because of shared ancestry? No! It turns out they are not that closely related, judging by phylogenies along the gene for a bunch of NLRs in Podospora. 7/n

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

We sequenced a panel of strains with known alleles, which can now be used to assign a phenotype to wild-type strains. With this information in hand, we determined that reactive alleles fold into two beta-propellers that likely embrace their cognate ligand HET-C like a clam. 6/n #AlphaFold

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

Of course, these HIC repeats are hard to sequence. We showed that assemblies of Illumina reads often recover broken or incorrect (!) allele reconstructions. But #PacBio and #Nanopore data get them just fine. 5/n #genomics

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

het-d/e have "high internal conservation" (HIC): their C-term domain is made out of nearly identical WD40 repeats. Only a few sites are different and evolve under diversifying selection. Concerted evolution (or something) homogenizes the repeats and leads to loss, gain, and shuffling of repeats. 4/n

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

In the model fungus #Podospora anserina, the het-d and het-e NLRs are highly polymorphic genes, whose products recognize different alleles of another gene, het-c. If two confronting strains have incompatible het-e/d and het-c alleles, a rejection reaction occurs. 3/n

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S. Lorena Ament @loreament.bsky.social · 02/07/2025

NOD-like receptors (NLRs) are intracellular proteins that play key roles in the innate immune system of plants and animals. But in fungi we know the function of only a few cases: they all work in heterokaryon incompatibility (rejection between different strains during vegetative fusion). 2/n

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