AmirAli Toghani
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amiralito.bsky.social
AmirAli Toghani
@amiralito.bsky.social
Biologist @thesainsburylab.bsky.social. Currently doing a PhD with @kamounlab.bsky.social

Curious about plant immune receptors, molecular evolution, and other stuff. 🌿💻 #evoMPMI

Find out more here:
amiralito.github.io
Up and ready! Find me at P-267 today for some molecular evolution and NLR biology! 🥬💻

You can also find the poster and preprint below 👇🏻

#2025ISMPMI
July 14, 2025 at 6:34 AM
14/ And finally, a teaser: We're gearing up to release deep-learning-based Helixer annotations and NLR sequences for 230 superasterid genomes on @datadryad & @ZENODO_ORG! Stay tuned.
February 26, 2025 at 4:55 PM
11/ Our evolutionary model? Sensor clades relying on the conserved NRC0 tend to have lower copy numbers and slower diversification—likely constrained. But those using other NRC helpers often expand dramatically, with higher copy numbers and greater diversification.
February 26, 2025 at 4:55 PM
10/ Mapping these sites onto predicted structures revealed distinct patterns: In Clade 1, they cluster in the CC domain, but in Clade 3, they dominate the LRR concave side. Coevolution happens at the LRRs but also elsewhere!
February 26, 2025 at 4:55 PM
9/ Next, we tested each clade for positive selection via PAML. While helpers show no strong signals, sensor clades tell a different story. Clade 3 stands out with 48 positively selected sites (mostly on the LRR), while Clade 1 has just 5, and Clade 2 has none!
February 26, 2025 at 4:55 PM
8/ Check this! Here is a phylogenetic overview of the sensor and helper AlphaFold 3 models. Phylogeny + Structural modeling! 🆒
February 26, 2025 at 4:55 PM
7/ Using AlphaFold 3, we found that NRC helpers can be modelled as resistosome-like complexes. But here's the twist—lettuce NRC sensors don’t form high-confidence oligomeric models, similar to what we saw in monocot NLR pairs!
www.biorxiv.org/content/10.1...
February 26, 2025 at 4:55 PM
6/ Big finding: Lettuce has a functional NRC network, and for the first time, we see a phylogenetic shift in helper dependency! Clade 1 sensors signal only through NRC0, clade 2 uses both helpers, and clade 3 relies solely on Ast-LsatNRC1.
February 26, 2025 at 4:55 PM
5/ Digging deeper—lettuce has two NRC type helpers: NRC0 (conserved in Asterids) and another, unique to Asterales, called Ast-LsatNRC1. Lettuce NRC sensors then split into three distinct phylogenetic clades.
February 26, 2025 at 4:55 PM
4/ We reannotated 40 Solanales + 29 Asterales genomes with the AI tool Helixer (see post #14). These lineages diverged ~100 MYA! Unlike Solanales (~50% of all NLRs), the NRC network shows much less expansion in Asterales (~6%).
February 26, 2025 at 4:55 PM
3/ The NRC network is an NLR immune network providing resistance to various pathogens in Asterid plants. We've studied its expansion and function in Solanales, but what about Asterales—especially in lettuce?
February 26, 2025 at 4:55 PM
2/ Lettuce is in the aster family #Asterales and a plant immunity model since the ’90s. Blake Meyers, @michelmorelab and colleagues classified NLR phylogenetic clades and introduced concepts like type I & II based on evolutionary rates.
February 26, 2025 at 4:55 PM