Genomic organization, domain assortments, and nucleotide-binding domain diversity of NLR proteins in Sordariales fungi

Fungi have NOD-Like receptors (NLRs), homologous to the innate immune receptors found in animals, plants and bacteria. Fungal NLRs are characterized by a great variability of domain organizations, but the identity of the nucleotide-binding domains, the genomic localization, and the factors associated with variation in the composition of repertoires of fungal NLRs are not yet fully understood. To better understand the variability of fungal NLR repertoires and the underlying determinants, we conducted a thorough analysis of genome data from the ascomycete order Sordariales. Using similarity searches based on hidden Markov models profiles for canonical N-terminal, nucleotide-binding, or C-terminal domains, we characterized 4613 NLRs in 82 Sordariales taxa. By examining the Helical Third section of the nucleotide-binding domains, we substantially improved their annotation. We demonstrated that fungi have NACHT domains of both NAIP-like and TLP1-like types, similar to animals. We found that the number of NLR genes was highly variable among Sordariales families, and independent of the stringency of defense mechanisms against genomic repeat elements. NLRs were organized in clusters in the majority of taxa, and the strong correlation between the number of NLRs and the number of NLR clusters suggested that organizing in clusters may contribute to repertoire diversification. Our work highlights the similarity of fungal and animal NLRs in terms of nucleotide-binding domain types, and between fungal and plant NLRs in terms of genomic organization in clusters. Our findings will aid in the comparative analysis of the patterns and processes of diversification of NLR repertoires in various lineages of fungi and between the different kingdoms and domains of life.Author summary: Fungi have NOD-Like receptors (NLRs), homologous to the innate immune receptors found in animals, plants and bacteria. Fungal NLRs are highly diverse, and how they evolve or function remains unclear. To explore this, we analyzed the genomes of 82 species from the fungal group Sordariales. Using advanced similarity searches, we identified 4,613 NLRs and found that the number of NLR genes varied widely between species, but this variation was not linked to the efficiency of mechanisms of defense against gene duplication. NLR genes often appeared in clusters in fungal genomes, similar to patterns seen in plant NLRs, and organization in clusters may contribute to NLR diversification over time. Some fungal NLRs also shared key features with animal NLRs, including two main types of NACHT nucleotide-binding domains (NAIP-like and TLP1-like). Our findings reveal surprising similarities in immune-like systems across fungi, animals, and plants. This work helps us understand how NLRs diversify and evolve across different forms of life.