Genomic and metabolic uniformity across diverse observed ecological contexts suggest that interactions of Pestalotiopsis formosana and P. neolitseae are context-dependent

A comparative genomic study found that isolates of the plant-associated fungi Pestalotiopsis formosana and P. neolitseae recovered from symptomatic, asymptomatic and dead plant tissues had broadly similar genomic and metabolic toolkits. The researchers found no consistent genome-scale differences that could explain the observed ecological labels, suggesting that these labels may reflect context-dependent interactions.

The researchers sequenced and annotated six new genomes: three isolates of P. formosana, two of P. neolitseae and one of P. sonneratiae. They compared these assemblies with four publicly available genomes, using Pseudopestalotiopsis fici W106-1 as an outgroup. Multi-locus analyses of ITS, tub2 and tef1-α confirmed the placement of the focal strains and prompted tentative revisions to the names assigned to some public genomes.

The nine Pestalotiopsis assemblies ranged from 46.25 to 48.35 million base pairs, while the outgroup was 51.91 million base pairs. GC content varied little among the Pestalotiopsis genomes, from 51.68% to 52.09%, and predicted protein counts ranged from 14,003 to 14,936. BUSCO assessments indicated more than 95% completeness for every assembly at the Fungi, Ascomycota and Sordariomycetes levels.

Ortholog analysis identified 12,021 core genes shared across all 10 strains, including the outgroup, and no ortholog group was consistently associated with the sampled ecological contexts. The three P. formosana isolates, obtained from dead grass, symptomatic Podocarpus tissue and asymptomatic Podocarpus leaves, shared essentially the same gene content.

Predicted secretomes contained 1,706 to 1,854 proteins, and predicted effectomes contained 425 to 447 proteins. Within P. formosana, the secretomes ranged from 1,841 to 1,854 proteins and the effectomes from 433 to 443, without a consistent increase or decrease linked to isolation context. These effectors were identified computationally, and their roles in host manipulation were not functionally validated.

Carbohydrate-active enzyme profiles were also similar, with 859 to 914 genes per genome and no clear separation among ecological groups. Strain-level statistical differences generally reflected small copy-number changes rather than broad functional shifts. CATAStrophy classified all strains as vasculartrophs, but this was a prediction based on CAZyme content rather than direct evidence of natural behaviour. Secondary-metabolite clusters, functional gene categories, candidate pathogenicity-related homologs and transposable elements likewise showed no consistent grouping by observed context.

Phenotypic assays demonstrated broad metabolic versatility alongside strain-level differences. In Biolog FF microplates, substrate richness ranged from 82 to 91, and all strains metabolized about 90% of the 95 tested substrates by 168 hours. The P. formosana isolate from dead material had higher average well colour development, 0.694, than the symptomatic and asymptomatic isolates, at 0.558 and 0.532, respectively. Growth on solid carbon-source media also varied by strain without a consistent association with isolation context.

The study was limited by its small and unbalanced sampling of species, hosts and ecological contexts. Its lifestyle categories were operational labels based on where and when isolates were recovered: symptomatic isolates were not necessarily confirmed primary pathogens, asymptomatic isolates could include latent or opportunistic organisms, and dead-material isolates could include secondary colonisers.

Accordingly, the results support context-dependent ecological expression as an interpretation rather than a demonstrated mechanism. They do not establish that the sampled organisms had identical genomes or metabolism, and they cannot determine whether unobserved genomic differences, gene regulation, host condition or environmental factors produced their observed associations.

Subject of Research: Comparative genomics of context-dependent ecological interactions in two Pestalotiopsis species

Article Title: Genomic and metabolic uniformity across diverse observed ecological contexts suggest that interactions of Pestalotiopsis formosana and P. neolitseae are context-dependent

Article References: Hsu, S.-Y., Mishra, B., Huang, H.-Y., Lin, Y.-C., Xu, Y.-C., Ploch, S., Hsu, C.-Y., Wang, J.-P., Elgorban, A. M., Alarjani, K. M., Thines, M., & Ariyawansa, H. A. (2026). Genomic and metabolic uniformity across diverse observed ecological contexts suggest that interactions of Pestalotiopsis formosana and P. neolitseae are context-dependent. IMA Fungus, 17, Article e192779. https://doi.org/10.3897/imafungus.17.192779

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.192779

Keywords: Pestalotiopsis formosana, Pestalotiopsis neolitseae, comparative genomics, fungal ecology, CAZymes, secretome, effectome, secondary metabolites, carbon utilization, Genomic, metabolic, uniformity