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Cryphonectriaceae is a diaporthalean family containing important plant pathogens of which is the most notorious one. An emerging stem blight disease on (Elaeocarpaceae) and was observed in Guangdong Province of China recently. Typical Cryphonectria blight-like symptoms including cankers on tree barks with obvious orange conidial tendrils were observed. Forty-eight isolates were obtained from diseased tissues and conidiomata formed on the hosts and . These isolates were further identified based on both morphology and molecular methods using the combined sequence data of the internal transcribed spacer (ITS) region, large subunit of the nrDNA (LSU), the translation elongation factor 1-alpha ( ) and DNA-directed RNA polymerase II second largest subunit (rpb2) genes. As a result, the fungus represents an undescribed genus and species within the family Cryphonectriaceae. Hence, is proposed herein to represent these isolates from diseased barks of and . differs from the other genera of Cryphonectriaceae in having dimorphic conidia. Further inoculation results showed that is the causal agent of this emerging blight disease in China, which can quickly infect and kill the hosts and .

Co-evolved plant pathogens play an important role in shaping natural ecosystems. However, plants used in agriculture and forestry have been distributed globally, and their associated pathogens have moved with them. Eucalypts constitute the largest component of global hardwood plantations, and they are increasingly plagued by numerous pathogens, all of which are inconsequential in the native forests. Eucalypts provide a particularly interesting model to study tree diseases because plantations have been established in countries where these trees are exotic but also in Australia adjacent to native eucalypt forests. These situations present opportunities for pathogen movement between the two systems. We present seven different scenarios considering pathogen movement, important disease epidemics, and biosecurity risks, illustrated with examples of well-known eucalypt pathogens and research largely from our laboratories. The overview shows that vigilant biosecurity is required to protect the biodiversity of native forests and the sustainability of eucalypt plantations.

In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.

Species of Cryphonectriaceae can occur as asymptomatic fungal endophytes in Melastomataceae trees and shrubs. One hypothesis suggests Chrysoporthe cubensis (Cryphonectriaceae) is an endophyte of the Melastomataceae that has undergone a host switch to infect species of Eucalyptus in South America. The potential for similar host switches by other species of the Cryphonectriaceae is exacerbated by native stands of Melastomataceae that grow alongside commercial plantations of Eucalyptus. We sought to determine the diversity of Cryphonectriaceae endophytic in Melastomataceae trees that occur naturally adjacent to Eucalyptus plantations in Colombia. Branch segments were taken from six different species in three genera of the Melastomataceae. A technique that simulated natural conditions was used to promote fruiting of endophytic Cryphonectriaceae. Taxa were identified using a phylogenetic species concept based on sequence data from the internal transcribed spacer and β-tubulin gene regions. Three species of Cryphonectriaceae, Aurapex penicillata, C. cubensis and C. inopina, were identified. We tested whether these endophytes were potential pathogens of Eucalyptus, and each species was mildly pathogenic. The results showed that at least six species of Melastomataceae are hosts of the Cryphonectriaceae in Colombia. They also emphasize the biosecurity risk of moving superficially healthy stem tissue of the Melastomataceae to new environments.

The family of Cryphonectriaceae (Diaporthales) contains many important tree pathogens and the hosts are wide-ranging. Tree species of Terminalia were widely planted as ornamental trees alongside city roads and villages in southern China. Recently, stem canker and cracked bark were observed on 2–6 year old Terminalia neotaliala and T. mantaly in several nurseries in Zhanjiang City, Guangdong Province, China. Typical conidiomata of Cryphonectriaceae fungi were observed on the surface of the diseased tissue. In this study, we used DNA sequence data (ITS, BT2/BT1 , TEF-1α , rpb2 ) and morphological characteristics to identify the strains from Terminalia trees. Our results showed that isolates obtained in this study represent two species of Aurifilum , one previously described species, A. terminali , and an unknown species, which we described as A. cerciana sp. nov. Pathogenicity tests demonstrated that both A. terminali and A. cerciana were able to infect T. neotaliala and two tested Eucalyptus clones, suggesting the potential for Aurifilum fungi to become new pathogens of Eucalyptus .

Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic repertoire enabling the colonization and exploitation of host species. Here, we have assembled >100 genomes across two related genera to identify key genomic determinants leading to the emergence of chestnut blight. We found subtle yet highly specific changes in the transition from saprotrophy to latent pathogenicity mostly determined by enzymes involved in carbohydrate metabolism. Large-scale genomic analyses of genes underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens. Emerging fungal pathogens are a threat to forest and agroecosystems, as well as animal and human health. How pathogens evolve from nonpathogenic ancestors is still poorly understood, making the prediction of future outbreaks challenging. Most pathogens have evolved lifestyle adaptations, which were enabled by specific changes in the gene content of the species. Hence, understanding transitions in the functions encoded by genomes gives valuable insight into the evolution of pathogenicity. Here, we studied lifestyle evolution in the genus Cryphonectria , including the prominent invasive pathogen Cryphonectria parasitica , the causal agent of chestnut blight on Castanea species. We assembled and compared the genomes of pathogenic and putatively nonpathogenic Cryphonectria species, as well as sister group pathogens in the family Cryphonectriaceae (Diaporthales, Ascomycetes), to investigate the evolution of genome size and gene content. We found a striking loss of genes associated with carbohydrate metabolism (CAZymes) in C. parasitica compared to other Cryphonectriaceae. Despite substantial CAZyme gene loss, experimental data suggest that C. parasitica has retained wood colonization abilities shared with other Cryphonectria species. Putative effectors substantially varied in number, cysteine content, and protein length among species. In contrast, secondary metabolite gene clusters show a high degree of conservation within the genus. Overall, our results underpin the recent lifestyle transition of C. parasitica toward a more pathogenic lifestyle. Our findings suggest that a CAZyme loss may have promoted pathogenicity of C. parasitica on Castanea species. Analyzing gene complements underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens. IMPORTANCE Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic repertoire enabling the colonization and exploitation of host species. Here, we have assembled >100 genomes across two related genera to identify key genomic determinants leading to the emergence of chestnut blight. We found subtle yet highly specific changes in the transition from saprotrophy to latent pathogenicity mostly determined by enzymes involved in carbohydrate metabolism. Large-scale genomic analyses of genes underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens.

Caryocar brasiliense Camb. (Ca. brasiliense) is a typical tree of the Brazilian Cerrado commonly known as pequi. The pequi fruits have a high potential for use in cosmetic and food industries. Due to its economic importance, during the fruiting period, numerous families living in the Cerrado biome benefit from direct fruit harvesting, which is often their only income source. There are no commercial plantations, and the only source of the pequi fruits is the natural Brazilian Cerrado. During a disease survey, an unknown fungus was observed on stem cankers of dying trees. The fungus has similar characteristics to the well-known family of canker pathogens, the Cryphonectriaceae. Thus, the aims of this study were to isolate and identify the fungus from those canker symptoms and assess its pathogenicity. Identification of the fungus was based on morphological characteristics as well as DNA sequence data. DNA from the internal transcribed spacer (ITS) regions, two fragments of the b-tubulin gene (BT1 and BT2), and large subunit of rDNA (LSU) was sequenced and compared with published sequences for 20 genera in the Cryphonectriaceae family. Pathogenicity tests were conducted on Ca. brasiliense seedlings. Morphological characterizations revealed that the fungus isolated from Ca. brasiliense differed from those typically found in the Cryphonectriaceae, especially for the presence of ostiolar septate single or branched hyphae. Phylogenetic analyses showed that this novel fungus from Ca. brasiliense grouped separately from other genera in the Cryphonectriaceae. Pathogenicity tests on Ca. brasiliense showed that the fungus is able to cause stem cankers. Taking all findings together, we propose that the pathogenic fungus isolated from Ca. brasiliense is a novel genus and a novel species in the Cryphonectriaceae, and thus, we named it as Capillaureum caryovora.

Cryptodiaporthe corni is the causal agent of a destructive disease called golden canker, which affects Cornus alternifolia, known as the pagoda or alternate-leaved dogwood. Due to the association between Cr. corni and pagoda dogwood, we sought to determine whether this fungus was capable of living as an endophyte in pagoda dogwood and causing this disease. Forty asymptomatic stems of plants growing in nature were sampled from five sites across Minnesota. Cryptodiaporthe corni was present in more than half (62.5%) of the stems. Asymptomatic nursery material also was sampled, and the fungus was isolated from a small percentage (20%) of them. Inoculations carried out in the field and greenhouse suggested the endophytic isolates of Cr. corni were capable of causing disease. Asymptomatic stems of trees in the field inoculated with non-colonized (control) grain seed developed golden canker as frequently as those inoculated with grain seed colonized by Cr. corni, suggesting that the fungus was already present in these plants. In greenhouse pathogenicity trials an isolate of Cr. corni obtained from an asymptomatic stem was capable of causing golden canker disease, thus demonstrating causality, fulfilling Koch's postulates. The taxonomic placement of Cr. corni within Cryphonectriaceae was determined. Phylogenetic analysis of the ITS rDNA and β-tubulin gene regions, along with morphological characteristics, suggested Cr. corni is distinct from other genera within this family. Therefore, we propose a new genus, Aurantioporthe, as well as the new combination, A. corni, to accommodate this species within Cryphonectriaceae.

Many species in the Cryphonectriaceae cause diseases of trees, including those in the genera Eucalyptus and Syzygium. During disease surveys on these trees in southern China, fruiting structures typical of fungi in the Cryphonectriaceae and associated with dying branches and stems were observed. Morphological comparisons suggested that these fungi were distinct from the well known Chrysoporthe deuterocubensis, also found on these trees in China. The aim of this study was to identify these fungi and evaluate their pathogenicity to Eucalyptus clones/species as well as Syzygium cumini. Three morphologically similar fungal isolates collected previously from Indonesia also were included in the study. Isolates were characterized based on comparisons of morphology and DNA sequence data for the partial LSU and ITS nuclear ribosomal DNA, β-tubulin and TEF-1α gene regions. After glasshouse trials to select virulent isolates field inoculations were undertaken to screen different commercial Eucalyptus clones/species and S. cumini trees for susceptibility to infection. Phylogenetic analyses showed that the Chinese isolates and those from Indonesia reside in a clade close to previously identified South African Celoporthe isolates. Based on morphology and DNA sequence comparisons, four new Celoporthe spp. were identified and they are described as C. syzygii, C. eucalypti, C. guangdongensis and C. indonesiensis. Field inoculations indicated that the three Chinese Celoporthe spp., C. syzygii, C. eucalypti and C. guangdongensis, are pathogenic to all tested Eucalyptus and S. cumini trees. Significant differences in the susceptibility of the inoculated Eucalyptus clones/species suggest that it will be possible to select disease-tolerant planting stock for forestry operations in the future.

Fungi in the Cryphonectriaceae are important canker pathogens of plants in the Melastomataceae and Myrtaceae (Myrtales). These fungi are known to undergo host jumps or shifts. In this study, fruiting structures resembling those of Cryphonectriaceae were collected and isolated from dying branches of Syzygium cordatum and root collars of Heteropyxis natalensis in South Africa, and from cankers on the bark of Tibouchina grandifolia in La Réunion. A phylogenetic species concept was used to identify the fungi using partial sequences of the large subunit and internal transcribed spacer regions of the nuclear ribosomal DNA, and two regions of the β-tubulin gene. The results revealed a new genus and species in the Cryphonectriaceae from South Africa that is provided with the name Myrtonectria myrtacearum gen. et sp. nov. Two new species of Celoporthe (Cel.) were recognised from La Réunion and these are described as Cel. borbonica sp. nov. and Cel. tibouchinae sp. nov. The new taxa were mildly pathogenic in pathogenicity tests on a clone of Eucalyptus grandis. Similar to other related taxa in the Cryphonectriaceae, they appear to be endophytes and latent pathogens that could threaten Eucalyptus forestry in the future.