Nine New Fungal Species Uncovered in China as Genomes Reshape Gnomoniopsis Family Tree

A team of mycologists working across China has described nine previously unknown species of the fungal genus Gnomoniopsis, drawing on a combination of classical microscopy, DNA-based phylogenetics, whole-genome sequencing and infection assays on detached chestnut leaves. The findings, published in the journal IMA Fungus, substantially expand both the known diversity of this poorly sampled genus and its meager genomic record, which before this study included publicly available whole-genome sequences for only four described species.

Gnomoniopsis is a genus of ascomycete fungi in the order Diaporthales that lives as parasites, endophytes and saprobes inside plant tissues. It is distributed worldwide and is most often associated with plants in the beech family (Fagaceae), as well as willows and members of the rose family. Some of its best-known members are serious plant pathogens: among the most typical are G. clavulata, G. smithogilvyi, G. daii and G. chinensis, and such pathogens can cause plant disasters on white oak (Quercus alba) and Chinese chestnut (Castanea mollissima), including in North America, imposing significant economic losses. According to the Index Fungorum database, 54 species of Gnomoniopsis had been recorded as of the study’s March 2026 access date, yet the genus has long been taxonomically unstable, its members notoriously difficult to tell apart because their microscopic features overlap heavily and spore sizes vary considerably.

The genus has a complicated taxonomic history. Berlese originally treated it as a subgenus of Gnomonia based on septate ascospore characters, but because those morphological traits proved unreliable, the group was temporarily merged back into Gnomonia. A turning point came in 2010, when Walker and colleagues used molecular phylogenetic analyses of the ITS, tub2 and tef1 gene regions to confirm that Gnomoniopsis forms a monophyletic group and formally re-established it as a distinct genus, compiling an identification key for 13 species. Research has since accelerated globally, and in China in particular, integrated morphological and molecular studies since 2018 have uncovered multiple new species across several provinces.

For the new study, the researchers collected diseased and decaying leaf samples in 2025 from forested areas of Yunnan, Hainan, Fujian, Northeast China and other regions. They isolated fungi from two very different sources: fresh leaf tissue bearing active necrotic lesions, which represents pathogenic populations, and naturally senescent, decaying leaves collected in the field, which represents saprophytic or endophytic material. Decomposed fragments with ambiguous symptoms were excluded to ensure accurate isolation sources. The isolation protocol was meticulous: five-millimeter squares of lesion tissue were surface-sterilized in 75% ethanol, 5% hypochlorous acid and repeated sterile-water rinses before being placed on potato dextrose agar and incubated in darkness at 25°C. Marginal hyphae were transferred repeatedly to fresh plates and purified by single-hypha isolation two to three times until axenic cultures were confirmed.

The nine new species were isolated from lesions on several host plants, including Embelia vestita, Lindera communis, Quercus griffithii and Castanopsis chinensis. The holotype collections trace to six host plants across five Chinese provinces: G. xiaoheijiangensis and G. embeliae from diseased leaves of Chinese chestnut (Castanea mollissima) in Yunnan’s Xiaoheijiang Forest Park, G. ledongensis from Quercus griffithii in Hainan, G. quercus from Quercus griffithii in Fujian, G. loropetali from Loropetalum chinense and G. qixiensis from Lindera glauca in Zhejiang, and G. yonganensis from Lindera communis in Fujian. Two species, G. yunvfengensis from Fujian’s Yunv Peak and G. conghuaensis from Guangdong’s Conghua District, came from decaying leaves without clear host information. According to the authors, the host set includes four hosts belonging to the Fagaceae, two to the genus Lindera in the Lauraceae, and one to the Primulaceae, extending the documented host and ecological range of the genus considerably.

To confirm that each isolate truly represented a distinct species, the team amplified and sequenced three standard barcoding loci—ITS, tef1 and tub2—and built a concatenated matrix of 2,450 aligned sequence sites from 50 isolates, using Apiognomonia errabunda as an outgroup. Of those sites, 1,191 were conserved, 241 were parsimony-uninformative and 1,018 were parsimony-informative. Maximum likelihood and Bayesian analyses both placed each new species in its own well-supported clade, and phylogenomic analyses of the nine new isolates corroborated the multi-locus topology. Pairwise sequence divergences against the closest known relatives ranged from subtle to striking: G. quercus differed from its nearest neighbor G. yunnanensis by less than one percent in ITS but up to 3.66 percent in tef1, whereas G. xiaoheijiangensis showed a 9.66 percent ITS divergence and a remarkable 61.93 percent difference in a tef1 region from its relative G. rossmaniae. Morphology reinforced the genetic separations, with conidiophore dimensions and conidial shapes—fusiform, ovate or even crescent-shaped—distinguishing closely related pairs.

The researchers also screened for hidden genetic exchange using the pairwise homoplasy index (PHI) test, which flags recombination between closely related taxa. All nine species yielded Φw values greater than the 0.05 critical threshold, indicating no significant recombination signals and supporting their recognition as genetically independent, validly delimited species under the genealogical concordance framework.

The genomic component of the study was the most significant leap forward. The team sequenced the whole genomes of one strain from each of the nine new species, adding them to four published Gnomoniopsis genomes retrieved from public databases and using Discula destructiva as an outgroup. A maximum likelihood phylogenomic tree built from 7,942 clusters of orthologous protein-coding genes resolved all taxa into well-supported monophyletic clades, with branch lengths reflecting clear interspecific divergence and strong intraspecific conservation. The annotated genomes revealed moderate variation in carbohydrate-active enzyme (CAZyme) content, ranging from 505 to 596 genes per strain. Glycoside hydrolases—the enzymes that dismantle complex plant carbohydrates—formed the dominant family, while carbohydrate-binding modules were completely conserved at exactly four copies in every isolate. In total, 727 secondary metabolite biosynthetic gene clusters were predicted across the nine genomes, varying from 67 to 94 clusters per strain and dominated by T1PKS, NRPS-like, terpene and NRPS types. Notably, the authors found no strong correlation between CAZyme counts and BGC abundance, suggesting that carbohydrate-degrading capacity and chemical diversity are shaped by different selective forces, and they detected several strain-specific cluster classes that may underpin lineage-specific host interactions.

To probe the disease potential of the new species, the team performed artificial inoculations on detached, healthy leaves of cultivated Chinese chestnut, a universal substrate chosen because obtaining intact disease-free foliage from each fungus’s native host was not practical. Wounded leaves were inoculated with mycelial plugs from each pure culture, while control leaves received blank agar plugs. Faint brown discoloration appeared around the inoculation wounds after three to four days and expanded into distinct water-soaked necrotic plaques, with no symptoms on any control leaf. The researchers then re-isolated fungi from lesion margins and confirmed by morphology and three-locus sequencing that the recovered strains matched the inoculated ones at 99 to 100 percent identity, satisfying Koch’s postulates under these experimental conditions. The authors are careful to frame the result: the assay demonstrates a general necrotrophic capacity on wounded Fagaceae tissue under laboratory conditions, not host-specific pathogenicity against each species’ original host, and the sexual reproductive stage was not observed for any of the nine new species.

The study’s authors argue that their results mark a shift in how Gnomoniopsis and similar genera should be classified. Single-locus approaches, they note, often lack the resolution to separate genetically close lineages and can produce clusterings inconsistent with boundaries supported by morphology, pathogenicity tests and recombination screening; multi-locus phylogeny or concatenated phylogenomic datasets are preferable. The nine new genome sequences more than double the publicly available genomic resources for the genus and provide a foundation for future work on adaptive evolution and species delimitation. At the same time, the team cautions that no definitive evolutionary or species-delimitation hypothesis should rest on the current genomic data alone: broader sampling, morphological comparison and physiological validation will be needed to refine the identification system. Given that two of the nine new species came from decaying leaves without clear host information, the authors suggest that many cryptic species and unexplored host associations likely remain hidden in less-studied plant lineages and microhabitats across China’s forests.

Subject of Research: Taxonomy, phylogeny and comparative genomics of nine new Gnomoniopsis fungal species from China

Article Title: Molecular and morphological characterization of nine new Gnomoniopsis species ( Diaporthales , Gnomoniaceae ): Genomic insights into evolution and phylogeny

Article References: Wang, X., Jiang, Y., Liu, W., Yan, X., Sheng, J., Ai, C., Liu, X., Zhang, X., Meng, Z., & Wang, S. (2026). Molecular and morphological characterization of nine new Gnomoniopsis species (Diaporthales, Gnomoniaceae): Genomic insights into evolution and phylogeny. IMA Fungus, 17, Article e208364. https://doi.org/10.3897/imafungus.17.208364

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.208364

Keywords: Gnomoniopsis, Diaporthales, fungal taxonomy, new species, phylogenomics, CAZymes, secondary metabolites, chestnut, China, plant pathology, Koch's postulates, species delimitation