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-Phylogenetic relationships among Melampsora species from aspen and white poplar. (A) ITS D 28S D 5 0 -CO1 maximum likelihood tree based on a K81uf D G substitution model (assuming a proportion of invariable site parameters equal to 0.014). (B) ITS D 28S maximum likelihood tree, including GenBank sequences (in bold) from rust strains infecting aspen and white poplar; tree reconstruction was based on a K81uf D G substitution model (assuming a gamma distribution of rate variation among sites equal to 0.024). (C) Attributes (including ITS and 28S sequences accession numbers) of 11 rust strains infecting white poplar and aspen downloaded from the GenBank database.
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Wide variation and overlap in morphological characters have led to confusion in species identification within the fungal rust genus Melampsora. The Melampsora species with uredinial-telial stages on white poplar and aspens are especially prone to misidentification. This group includes the Melampsora populnea species complex and the highly destructi...
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Context 1
... likelihood (ML) analyses of each separate data set, using the reciprocal 70 % bootstrap threshold ( Feau et al. 2006Feau et al. , 2007, resulted in topologically congruent trees (data not shown). The phylogenetic analysis conducted on the combined ITS, 28S, and 5 0 -CO1 data sets resulted in apparent good level of resolution with only one single tree obtained (ÀLn ¼ 3745) ( Fig 4A). The analysis resolved five different phylogenetic species with a bootstrap support (BS) up to 90 %. ...
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... four species of the M. populnea complex were partially resolved: M. larici-tremulae and M. pinitorqua were unresolved within one single and well-supported (BS ¼ 100 %) monophyletic clade; M. rostrupii (strain 01G1) and M. magnusiana were also found unresolved in one statistically supported clade (BS ¼ 99 %) and appeared more related to the M. aecidioides clade (BS ¼ 100 %) than the other members of the complex. Eleven additional ITS and 28S sequences representing four additional Melampsora species collected on white poplar and aspen were downloaded from the non-redundant GenBank database and included in an ITS/28S ML phylogeny (Fig 4B-C). ML phylogenetic reconstruction resulted in six trees of equal length (ÀLn ¼ 2254) (Fig 4B). ...
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... additional ITS and 28S sequences representing four additional Melampsora species collected on white poplar and aspen were downloaded from the non-redundant GenBank database and included in an ITS/28S ML phylogeny (Fig 4B-C). ML phylogenetic reconstruction resulted in six trees of equal length (ÀLn ¼ 2254) (Fig 4B). No additional phylogenetic species was resolved following the addition of these 11 taxa. ...
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... a phylogenetic perspective, we acquired strong evidence that M. aecidioides is closely related but clearly distinct to both M. rostrupii and M. magnusiana (K2P distance ¼ 0.005). The two former species remained undifferentiated in one single monophyletic clade (Fig 4A; BS ¼ 99 %). Pairwise genetic divergence among M. magnusiana and M. rostrupii showed a small divergence between these species (K2P distance ¼ 0.0005; two SNPs over the 2130 nucleotides analysed), quite similar to the average within species divergences (K2P distance ¼ 0.0003) in the other Melampsora species considered. ...
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The species-level identification of sterile and/or arthroconidium-forming filamentous fungi presumed to be basidiomycetes based upon morphological or physiological features alone is usually not possible due to the limited amount of hyphal differentiation. Therefore, a reliable molecular approach capable of the unambiguous identification of clinical...
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... For plant pathogenic organisms, either a single sorus from a strain can be excised from the infected host tissue (Feau et al. 2009) or both plant and pathogen DNA can be isolated together (Datlof et al. 2017). The latter has the advantage of requiring no culture, but DNA from other fungal species may be extracted alongside the target DNA . ...
... Melampsora pathogens have five sporulation stages in their life cycle tied to two alternate hosts (Newcombe and Chastagner, 1993;Mattila et al., 2001;Pei et al., 2005;Feau et al., 2009;Hacquard et al., 2013;Li et al., 2016). In temperate and boreal forests, a salicaceous host (poplar or willow depending on the rust species) becomes infested with dikaryotic (n+n) aeciospores. ...
... Throughout the growth season, the aeciospores develop and vigorously multiply on the leaves, initially as orange urediniospores (n+n) that subsequently become melanized "early (n+n)" and then (on senesced leaves) "late (2n)" teliospores. The teliospores are rich in lipids and glycogen, which enables the pathogen to tolerate winter frost (Feau et al., 2009). After undergoing karyogamy and meiosis, haploid basidiospores (n) are formed, which can then infect the alternate host (which may be a coniferous tree). ...
... Visual scores are also frequently used to assess resistance properties in common garden experiments (Newcombe and Chastagner, 1993;Albrectsen et al., 2010a;Robinson et al., 2012). Additionally, molecular detection and quantification techniques are increasingly used to analyze individual trees or small groups of trees (Feau et al., 2009;Ioos et al., 2010;Tan et al., 2010). Fungi share a conserved ITS rDNA sequence that can be amplified using specific primers, enabling PCR-based molecular verification and quantification of fungal infestations (Bourassa et al., 2005;Husson et al., 2013;Boutigny et al., 2013a;Boutigny et al., 2013b;Bergeron et al., 2019;Siddique et al., 2022). ...
Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.
... For plant pathogenic organisms, either a single sorus from a strain can be excised from the infected host tissue (Feau et al. 2009) or both plant and pathogen DNA can be isolated together (Datlof et al. 2017). The latter has the advantage of requiring no culture, but DNA from other fungal species may be extracted alongside the target DNA . ...
... Notes -Both Ceropsora and Melampsora are distinctive from the rest families in Caeoma-type aecia, Uredo-type uredinia, and telia with sessile and unicellular teliospores (Figure 1; Sydow and Sydow 1915;Cummins and Hiratsuka 2003;Aime and Taggart 2021). Two genera constitute the family Melampsoraceae, which is confirmed to be monophyly by Tian et al. (2004), Feau et al. (2009), and Zhao et al. (2017 Notes -Milesina, Naohidemyces and Uredinopsis were classified in Pucciniastraceae based on their teliospores that are embedded in the host tissue and the Peridermium-type aecia (Cummins and Hiratsuka 1984;Cummins and Hiratsuka 2003). Phylogenetically, Milesia, Naohidemyces and Uredinopsis clustered in one phylogenetic group, and separated from Hyalopsora, Melampsorella, Melampsoridium, Pucciniastrum and Thekopsora (Figure 1). ...
... Our previous and current studies on the phylogeny of Pucciniales, particularly those in the Melampsorineae, have revealed that morphological characters, especially spore-producing structures throughout the whole life cycle, such as basidia spermogonia, aecia, uredinia and telia, were phylogenetically more informative at higher taxonomic ranks (family level). By contrast, spore morphologies such as basidiospores, spermatia, aeciospores, urediniospores and teliospores, were phylogenetically more informative at lower taxonomic rank (species level) (Tian et al. 2004;Crane et al. 2005;Feau et al. 2009, Beenken 2014Zhao et al. 2015Zhao et al. , 2017. These spore-producing structures represent early diverged morphological characters, while spore morphologies have already been proved to be recently diverged characters by our continuous investigations (Figure 1; Zhao et al. 2020Zhao et al. , 2021. ...
Rust fungi in the order Pucciniales represent one of the largest groups of phytopathogens, which occur on mosses, ferns to advanced monocots and dicots. Seven suborders and 18 families have been reported so far, however recent phylogenetic studies have revealed para- or polyphyly of several morphologically defined suborders and families, particularly in Melampsorineae. In this study, a comprehensive phylogenetic framework was constructed based on a molecular phylogeny inferred from rDNA sequences of 160 species belonging to 16 genera in Melampsorineae (i.e. Chrysomyxa, Cerospora, Coleopuccinia, Coleosporium, Cronartium, Hylospora, Melampsora, Melampsorella, Melampsoridium, Milesina, Naohidemyces, Pucciniastrum, Quasipucciniastrum, Rossmanomyces, Thekopsora, Uredinopsis). Our phylogenetic inference indicated that 13 genera are monophyletic with strong supports, while Pucciniastrum is apparently polyphyletic. A new genus, Nothopucciniastrum was therefore established and segregated from Pucciniastrum, with ten new combinations proposed. At the family level, this study further demonstrates the importance of applying morphologies of spore-producing structures (basidia, spermogonia, aecia, uredinia and telia) in higher rank taxonomy, while those traditionally applied spore morphologies (basidiospores, spermatia, aeciospores, urediniospores and teliospores) represent later diverged characters that are more suitable for the taxonomy at generic and species levels. Three new families, Hyalopsoraceae, Nothopucciniastraceae and Thekopsoraceae were proposed based on phylogenetic and morphological distinctions, towards a further revision of Pucciniales in line with the phylogenetic relationships.
... More recently, molecular data has revealed interspecific relationships in Melampsora, and taxonomic identities have been resolved via rDNA phylogenies (Zhao et al. 2020). There have been several systematic studies at the species level in Melampsora (Tian et al. 2004, Feau et al. 2009, Zhao et al. 2015c. Molecular barcodes for identification at both generic and species level are available. ...
... Among the 212 reported species, nucleotide sequences from 71 species of Melampsora are presently available. Tian et al. 2004, Feau et al. 2009, Zhao et al. 2015c, Zhao et al. 2017, Zhao et al. 2020. ...
This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta , Cadophora , Celoporthe , Cercospora , Coleophoma , Cytospora , Dendrostoma , Didymella , Endothia , Heterophaeomoniella , Leptosphaerulina , Melampsora , Nigrospora , Pezicula , Phaeomoniella , Pseudocercospora , Pteridopassalora , Zymoseptoria , and one genus of oomycetes, Phytophthora . This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names.
... Traditional identification of freshwater hyphomycetes was based on morphological characters, especially conidiophores, conidiogenous cells and conidia [6]. However, the morphology of some species is quite similar and some morphological characters overlap between taxa and, therefore, morphology alone is not sufficient for reliable identification at lower taxonomic levels [31][32][33]. Molecular data has significantly solved this problem, allowing a better species classification of fungi [31,[32][33][34]. ...
... However, the morphology of some species is quite similar and some morphological characters overlap between taxa and, therefore, morphology alone is not sufficient for reliable identification at lower taxonomic levels [31][32][33]. Molecular data has significantly solved this problem, allowing a better species classification of fungi [31,[32][33][34]. For example, species of the freshwater hyphomycetes genus Cancellidium, are quite similar in morphology and previous studies have identified them as the same species. ...
Freshwater hyphomycetes are a highly diverse group of fungi with a worldwide distribution and have been mostly reported from tropical and subtropical regions. During investigations of freshwater fungi from the Greater Mekong subregion in China and Thailand, sixteen freshwater hyphomycetes (three of them belong to the class Dothideomycetes while thirteen belong to the class Sordariomycetes) were collected. Based on morphology and multi-gene phylogenetic analyses, Neospadicoides thailandica, Pseudodactylaria aquatica, Sporidesmium nujiangense, Tetraploa thailandica, Vamsapriya aquatica and Wongia fusiformis are described as new species; Aquapteridospora bambusinum is proposed as a new combination; Acrodictys liputii, Chloridium gonytrichii, Pseudoberkleasmium chiangmaiense, Pleomonodictys capensis, Sporidesmium aturbinatum and Vamsapriya indica are reported as new country records; and Sporidesmium tropicale, Sporoschisma chiangraiense and Sporoschisma longicatenatum are introduced as three new collections. In addition, a checklist of freshwater fungi from China over the last five years is also provided.
... These are from the Basidiomycetes and the Ascomycetes. Generally, estimates of the hazardous potential of different species of a genus can be difficult, and morphological determination can mismatch the underlying phylogeny [13,34]. Therefore, we identified clades that may be hazardous if the genus is known to bear mainly pathogenic species or is nested into hazardous species/genera in cases of species that are unknown to genus level. ...
Woody fruit which stay on ornamental plants for a long time may present a risk of infection to other organisms due to the presence of pathogens on their surface. We compared the microbe communities on the fruit surfaces of garden ornamental Gardenia thunbergia Thunb. with those on other surfaces in the study region. As Gardenia fruit contain antifungal substances, the focus of this study was on the fungal communities that exist thereon. We used Illumina sequencing to identify Amplicon Sequence Variants (ASV) of the internal transcribed spacer 2 (ITS2) of the ribosomal RNA. The microbial communities of the Gardenia fruit are distinct from the communities from the surrounding environments, indicating a specialized microhabitat. We employed clustering methods to position unidentified ASVs relative to known ASVs. We identified a total of 56 ASVs representing high risk fungal species as putative plant pathogens exclusively found on the fruit of Gardenia. Additionally, we found several ASVs representing putative animal or human pathogens. Those pathogens were distributed over distinct fungi clades. The infection risk of the high diversity of putative pathogens represented on the Gardenia fruit needs to be elucidated in further investigations.
... (Tian et al. 2004). A molecular phylogenetic study, however, showed that M. aecidioides was genetically distinct from the latter two species (Feau et al. 2009). (Tian et al. 2004). ...
... (Tian et al. 2004). A molecular phylogenetic study, however, showed that M. aecidioides was genetically distinct from the latter two species (Feau et al. 2009). Morphology-Urediniospores obovoid, obovoid-ellipsoid or broadly ellipsoid, and 22-29 × 16-25 µm in size; the wall ca. ...
The rust fungus survey was carried out in 8–12 September 2016 in the Liupanshan Mountains,
adjacent areas, and part of Mt. Helanshan, Ningxia Hui Autonomous Region, China. We herein report thirty-two species in eleven teleomorphic genera, Coleosporium, Gymnoconia, Melampsora, Melampsoridium, Miyagia, Phragmidium, Puccinia, Pucciniastrum, Quasipucciniastrum, Tranzschelia, and Uromyces, and one anamorphic genus Uredo.
... isolates (C16, C17), and a C. perlucidum isolate formed a group with American isolates (SW287, SW271, and CL024) of Chaetomium spp., thereby supporting the close relationships among these isolates. ITS has been successfully used for species discrimination of six genera in Zygomycetes (Schwarz et al. 2006), Trichoderma, and Hypocrea in Ascomycota (Druzhinina et al. 2005) and Cortinarius section Calochroi (Frøslev et al. 2007) and Melampsora (Feau et al. 2009) in Basidiomycota. ...
Since Gustav Kunze described and published genus Chaetomium in Mykologische Hefte (Leipzig) in 1817, the genus attracted an immense interest worldwide. Chaetomium is a diverse genus occurring worldwide; species from this genus are capable of colonizing various biotopes, such as soils, marine, animal dung, hair, textiles, plant tissues, seeds, and other substrates rich in cellulose. Chaetomium species are the largest genus of saprophytic ascomycetes, which belongs to the Chaetomiaceae family. The taxonomy of Chaetomium has been studied by several authors. Since the establishment of the genus, more than 400 species have been described, many of which were synonymized/excluded, and only 273 Chaetomium species were accepted according to Index Fungorum Partnership (IFP 2019). Due to the diversity of species and of inhabiting environments, Chaetomium spp. might conceive diverse biosynthetic gene clusters, which transform into various secondary metabolites (the fungi languages) to adapt to different ecological environments. Until now, more than 200 compounds with a wide range of bioactive effects have been isolated from Chaetomium spp., but compared with its richness of species, more bioactive secondary metabolites might be found in this member of fungi. Therefore, together with its ubiquitous nature, these species have great significant impacts on ecosystems, agriculture, food production, biotechnology, and human and animal health. The goal of this chapter is to represent the biodiversity of genus Chaetomium in a wide range of environmental habitats including deserts, salterns, agricultural, mangrove, living plants and animals, air, decayed wood, stones, and human. It is intended, in this chapter, to report on the accepted Chaetomium species and to propose a provisional key to their identification.
... Additional loci consistently increase delimitation success across a wide range of taxa, supporting a multilocus integrative approach (Dupuis et al., 2012). Multilocus DNA barcoding that combines cytochrome oxidase 1 and ribosomal RNA from the internal transcribed spacer (ITS) or the large subunit (28S) has proven successful in identifying fungal and oomycete plant pathogens (Feau, Vialle, Allaire, Maier, & Hamelin, 2011;Robideau et al., 2011) and discovering misidentified plant pathogens in public collections, which are critical references for identifying new potential invasive species ( Feau et al., 2009). ...
The world's forests face unprecedented threats from invasive insects and pathogens that can cause large irreversible damage to the ecosystems. This threatens the world's capacity to provide long‐term fiber supply and ecosystem services that range from carbon storage, nutrient cycling, and water and air purification, to soil preservation and maintenance of wildlife habitat. Reducing the threat of forest invasive alien species requires vigilant biosurveillance, the process of gathering, integrating, interpreting, and communicating essential information about pest and pathogen threats to achieve early detection and warning and to enable better decision‐making. This process is challenging due to the diversity of invasive pests and pathogens that need to be identified, the diverse pathways of introduction, and the difficulty in assessing the risk of establishment. Genomics can provide powerful new solutions to biosurveillance. The process of invasion is a story written in four chapters: transport, introduction, establishment, and spread. The series of processes that lead to a successful invasion can leave behind a DNA signature that tells the story of an invasion. This signature can help us understand the dynamic, multistep process of invasion and inform management of current and future introductions. This review describes current and future application of genomic tools and pipelines that will provide accurate identification of pests and pathogens, assign outbreak or survey samples to putative sources to identify pathways of spread, and assess risk based on traits that impact the outbreak outcome.
