Genome-wide analysis and evolutionary history of the Necrosis and Ethylene-inducing peptide 1-like protein (NLP) superfamily across the Dothideomycetes class of fungi

Abstract

Necrosis and Ethylene-inducing peptide 1-like proteins (NLPs) are broadly distributed across bacteria, fungi and oomycetes. Cytotoxic NLPs are usually secreted into the host apoplast where they can induce cell death and trigger plant immune responses in eudicots. To investigate the evolutionary history of the NLPs, we accessed the genomic resources of 79 species from 15 orders of Dothideomycetes. Phylogenetic approaches searched for biased patterns of NLP gene evolution and aimed to provide a phylogenetic framework for the cytotoxic activities of NLPs. Among Dothideomycetes, the NLP superfamily sizes varied, but usually contained from one to six members. Superfamily sizes were higher among pathogenic fungi, with family members that were mostly effector NLPs. Across species, members of the NLP1 family (Type I NLPs) were predominant (84%) over members of the NLP2 family (Type II NLPs). The NLP1 family split into two subfamilies (NLP1.1 and NLP1.2). The NLP1.1 subfamily was broadly distributed across Dothideomycetes. There was strong agreement between the phylogenomics of Dothideomycetes and the phylogenetic tree based on members of the NLP1 subfamilies. To a lesser extent, phylogenomics also agreed with the phylogeny based on members of the NLP2 family. While gene losses seem to have shaped the evolutionary history of NLP2 family, ancient gene duplications followed by descent with modification characterized the NLP1 family. The strongest cytotoxic activities were recorded on NLPs of the NLP1.1 subfamily, suggesting that biased NLP gene retention in this subfamily favored the cytotoxic paralogs.

The Necrosis- and Ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola

“…We found evidence for a phylogeny-based classification of the NLP types into distinct NLP families: NLP1, NLP2, and NLP3. In addition to the consistently small size of the NLP superfamily among Dothideomycetes, we found that the NLP1 family was the most predominant family across a variety of taxa and could be split further into two subfamilies: NLP1.1 and NLP1.2 (Dal’Sasso et al 2022). Amongst 79 species of Dothideomycetes, Corynespora cassiicola was one of the few species in which the members of both NLP1.1 and NLP1.2 subfamilies were present simultaneously.…”

“…Protein annotation and assemble of NLP homologues were performed as previously described for Dothideomycetes (Dal'Sasso et al 2022). The predicted proteomes of the Corca set was annotated using PfamScan with Pfam v32.0 (El-Gebali et al 2019) and InterProScan v5.30.69 (Jones et al 2014) with the following eight parameters: SMART-7.1, SUPERFAMILY-1.75, ProDom-2006.1, CDD-3.16, TIGRFAM-15.0, Pfam v31.0, Coils-2.2.1, and Gene3D-4.2.0. Secreted proteins were defined by the presence of a signal peptide (according to SignalP v4.1; Petersen et al 2011) and the absence of transmembrane domains (according to TMHMM v2.0; Krogh et al 2001).…”

“…Accumulation of mutations as a source of genetic variability exposes effector genes to mutations with both beneficial and deleterious effects (Fouché et al 2018). Rapid evolution leading to an excess of mutations could eventually lead to loss-of-function of the Cc_NLP1.2A in C. cassiicola and would help to explain the rare occurrence of Cc_NLP1.2A homologues across the Dothideomycetes (Dal'Sasso et al 2022).…”

“…Amongst 79 species of Dothideomycetes, Corynespora cassiicola was one of the few species in which the members of both NLP1.1 and NLP1.2 subfamilies were present simultaneously. Namely, the genome of C. cassiicola possesses one gene that is member of the NLP1.1 subfamily and two genes that are members of the NLP1.2 subfamily (Dal'Sasso et al 2022).…”

“…Previously, we investigated the evolutionary history of NLPs across the Dothideomycetes, the largest class of ascomycetes (Dal’Sasso et al 2022). We found evidence for a phylogeny-based classification of the NLP types into distinct NLP families: NLP1, NLP2, and NLP3.…”