Proteins containing the SQS-PSY domain, which include squalene synthetase (SQS), phytoene synthetase (PSY), and NDUFAF6, are functionally important and widely distributed in plants and animals. However, they have not been previously reported in nematodes. In this study, we identified a gene (Minc31999) encoding an SQS-PSY domain-containing protein in the root-knot nematode Meloidogyne incognita. In silico comparison and enzymatic assays of the recombinant protein indicated that this nematode protein is a putative NDUFAF6 homolog. Phylogenetic analysis revealed that this protein is evolutionarily conserved within the Nematoda phylum. RT-qPCR analysis showed that Minc31999 is highly expressed during the early infection stage of M. incognita. Targeting the nematode gene Minc31999 via host-induced gene silencing (HIGS) significantly hindered nematode development and virulence. In contrast, heterologous expression of Minc31999 in Arabidopsis thaliana disrupted normal plant development and increased host susceptibility to nematode infection. Transcriptomic profiling (RNA-seq) of these transgenic plants prior to infections showed a widespread differential expression of genes across multiple metabolic pathways. We propose that this nematode SQS-PSY domain-containing protein may function as an effector that rewires host secondary metabolism to establish a parasitic relationship. Our study elucidates a novel strategy in nematode–plant interactions and advances our understanding of the functional evolution of SQS-PSY domain-containing proteins.

Trichoderma longibrachiatum is a filamentous fungus that functions as a biocontrol agent against multiple plant diseases. However, the lack of a genetic transformation system has hindered studies on gene function and the underlying biocontrol mechanisms in this species. In this study, protoplast preparation conditions were optimized using single-factor experiments and response surface methodology, yielding 2.05 × 10⁷ protoplasts/g. PEG-mediated transformation yielded a GFP-labeled strain (GFP-40418). This strain enhanced resistance against Meloidogyne incognita, with root galling decreased by 47.6%. Treatment with GFP-40418 enhanced the activities of antioxidant enzymes, including PAL, POX, SOD, PPO, APX, and CAT. Plants treated with GFP-40418 alone showed the highest expression value, with relative transcriptional levels of PR2, Pal1, LOX, MYC2, ETR1, and ACO1 that were 29.62, 5.76, 7.30, 3.64, 4.79, 9.99-fold higher in comparison with control plants, respectively. These findings provide a genetic platform for exploring the gene functions of T. longibrachiatum 40418 and validate its biocontrol prospect against root-knot nematodes.