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Boxplot of germ pore numbers of urediniospores of 12 Milesina spp. and four sections. For each species 120 spores from two (M. magnusiana), three (M. feurichii) or four (all other species) specimens were evaluated. Median, whisker, quantile and outliers (dots) are shown.
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Species of rust fungi of the genus Milesina (Pucciniastraceae, Pucciniales) are distributed mainly in northern temperate regions. They host-alternate between needles of fir ( Abies spp.) and fronds of ferns (species of Polypodiales). Milesina species are distinguished based on host taxonomy and urediniospore morphology. In this study, 12 species of...
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Fragmented and degraded DNA is pervasive among museum specimens, hindering molecular phylogenetics and species identification. Mini-barcodes, 200–300-base-pair (bp) fragments of barcoding genes, have proven effective for species-level identification of specimens from which complete barcodes cannot be obtained in many groups, but have yet to be test...
Citations
... Phylogenetic analysis LSU and ITS sequences were used to reconstruct the phylogenetic position of the IHLR taxon observed across the southeastern United States, notably resolving its position within the genus Melampsoridium. Sequences obtained in this study and voucher sequences from previously published work (Liang et al., 2006;McKenzie et al., 2013;Bubner et al., 2019) were aligned using the MUSCLE (Edgar, 2004) plugin for GENEIOUS 10. Sequences were visually edited to treat ambiguities and sequencing errors. ...
In the late fall of 2018, foliar rust (referred to as ironwood/hophornbeam leaf rust [IHLR]) was discovered in several counties in Florida, United States, on ironwood (Carpinus caroliniana) and hophornbeam(Ostrya virginiana), bothmembers of the Betulaceae. Uredinia were observed on leaves and, in some cases, samaras of both species at numerous locations on trees of all age classes. Similar reports across the southeastern United States (Georgia, the Carolinas, Tennessee, and Texas) were detected the following year, with European hornbeam (Carpinus betulus) being reported as an additional host, while Ostrya virginiana var. guatemalensis in El Salvador was also discovered showing signs of uredinial infection. Field observations and analyses ofmorphological data obtained with light and scanning electron microscopy on IHLR and related Melampsoridium herbarium samples and combined molecular data from the ITS and LSU loci indicate that (i) IHLR across samples from the southeastern United States and El Salvador belong to the same taxon; (ii) IHLR is closely a liated to M. asiaticum; and (iii) some taxonomic modifications might be necessary at the genus level. No alternative (gametophyte) host has been identified, and the rust is likely overwintering in the uredinial stage. This disease represents a novel leaf pathogen on these hosts in North America, and efforts are needed to monitor future disease epidemiology and impacts on these native and cultivated tree species.
... The age of the specimens in L eveill e-Bourret et al., (2021) was comparable with that of the present study; however, they did not evaluate specimens from the early 1800s. Sequencing the ITS2 region of herbarium specimens is especially promising as this region has enough interspecies variation to adequately decipher the different species of rusts (McTaggart & Aime, 2018;Bubner et al., 2019;Chen et al., 2022). It should be noted the ITS region in rust fungi has been noted to have several problematic issues (i.e. it is difficult to amplify with nonspecific primers and contains Fig. 4 ITS haplotype frequency of Puccinia suaveolens specimens throughout the world. ...
Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera.
We then obtained sequences from an economically important biological control agent, Puccinia suaveolens, to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range.
Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial–temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi.
In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant–microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.
... and Rosaceae rusts within Coleosporiaceae using light and electron microscopy. These features have recently been documented for species and sectional delimitation in Milesina (Bubner et al. 2019) but have not been considered in morphological studies of P. epilobii s. lat. (Klebahn 1900(Klebahn , 1914Bisby 1916;Pady 1933) and the rusts on Rosaceae (Ziller 1974;Helfer 2005;Qi et al. 2019). ...
... Sequences were aligned with the CrustalW algorithm implemented in the programme Bio Edit, version 7.1.3.0 (Hall 1999), using the standard parameters offered by the programme. Two sequences of Milesina kriegeriana (Bubner et al. 2019) were used as the outgroup. Alignments were used for phylogenetic reconstruction by three different methods: ...
... Germ pores of urediniospores of Pucciniastrum epilobii s. lat. were visualised by the method described in Bubner et al. (2019). For scanning electron microscopy (SEM), uredinia and urediniospores of dried specimens of P. epilobii s. lat. ...
Using molecular phylogenetic analyses (ITS) and morphological data obtained from light and electron microscopy, some European and North American species and genera placed or formerly placed in the genus Pucciniastrum in the Coleosporiaceae and Pucciniastraceae (Pucciniales) were taxonomically revised. The ITS analyses confirmed recent familiar concepts based on less variable markers except for the genus Hyalopsora. The family Pucciniastraceae is characterized by Abietoideae (Abies, Tsuga) aecial hosts. Pucciniastrum is described as a genus that consists of host-alternating species forming aecia on needles of Abies hosts, with special features of aeciospore morphology, and Onagraceae telial hosts. Other genera in the Pucciniastraceae are Calyptospora, Melampsorella, and additional taxa, which are currently provisionally placed in Pucciniastrum, but must be revised in future studies. Pucciniastrum epilobii (s. lat.), the type species of Pucciniastraceae, represents at least two species with different life cycles and urediniospore characteristics and is lecto-and epitypified. The family Coleosporiaceae, characterized by Pinoideae (Pinus) and Piceoideae (Picea) aecial hosts, contains Rosaceae rusts from three well-supported clades represented by three genera, Thekopsora, Quasipucciniastrum, and Aculeastrum gen. nov. Aculeastrum is characterized by coarsely arcuate ostiolar peridial cells and infects Rubus spp. telial hosts. The following new taxonomic combinations are proposed: Calyptospora ornamentalis comb. nov., Quasipucciniastrum ochraceum comb. nov., Q. potentillae comb. nov, Aculeastrum americanum comb. nov., and A. arcticum comb. nov. The results are discussed with emphasis on future studies in Pucciniastrum and the P. epilobii complex and on nomenclatural changes necessary for rust fungi due to the Shenzhen Code.
... The LSU has been used as an alternative barcode for rust fungi instead, alone or with other markers (e.g., Bennett et al. 2011;McTaggart et al. 2015a;Maier et al. 2016;Ebinghaus et al. 2018). Depending on the genus, different barcodes may provide better species resolution (see discussion in Bubner et al. 2019). McTaggart and Aime (2018) wrote for Coleosporium that the ITS2 spacer region may vary where LSU is unable to differentiate among species. ...
Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidiomycota, the second largest phylum of Fungi that contains some of the best known species of mushrooms, rusts, smuts, and jelly fungi. In general, best practice is to delimitate species, publish new taxa, and conduct taxonomic revisions based on as many independent lines of evidence as possible, that is, by applying a so-called unifying (or integrative) conceptual framework. However, the types of data used vary considerably from group to group. For this reason we discuss the different classes of Basidiomycota, and for each provide: (i) a general introduction with difficulties faced in species recognition, (ii) species concepts and methods for species delimitation, and (iii) community recommendations and conclusions.
... Sequence data of other rust fungi were chosen based on those previously examined for the phylogeny of rust fungi (McTaggart, Geering, & Shivas, 2014;Beenken, 2017;Aime, Bell, & Wilson, 2018;Bubner, Buchheit, Friedrich, Kummer, & Scholler, 2019;Martins Jr., Sakuragui, Hennen, & Carvalho Jr., 2019;Ono et al., 2020;Aime & McTaggart, 2021) and included to infer the taxonomic relationships among other rust fungi (Table 2). In these analyses, Cae- A d v a n c e P u b l i c a t i o n A d v a n c e P u b l i c a t i o n oma torreyae Bonar (AF522183) was chosen as the outgroup (McTaggart, Geering, & Shivas, 2014;Beenken, 2017). ...
The rust fungi (Pucciniales) that infect ferns, early diverging vascular plants, are neither “primitive” nor monophyletic, as once hypothe- sized. The neotropical fern pathogen, Puccinia lygodii (Pucciniaceae), specializes on species of Lygodium. Lygodium is believed to have evolved in a period ca. 211 mya, which is after the evolution of the temperate fern rust fungi that parasitize later diverged ferns. Puccin- ia lygodii is the only rust species in the genus Puccinia known to infect ferns, the majority of which infect flowering plants. In this study we examined multiple new and herbarium specimens of P. lygodii and reconstructed its phylogenetic history with data generated from the 28S nuclear rDNA repeat. Puccinia lygodii is the sister species to another neotropical fern rust, Desmella aneimiae (Pucciniaceae), which also infects early diverged leptosporangiate fern species, and the new combination D. lygodii is made. Interestingly, P. lygodii and D. aneimiae differ primarily in sorus structure, i.e., subepidermal in the former vs. suprastomatal in the latter fungus. Characters such as suprastomatal sori and probasidia that germinate without dormancy are now known to represent a suite of adaptations that have been derived multiple times within Pucciniales, most likely in response to tropical climates.
... This renders their accurate identification based on phenotype often difficult or even impossible (Lücking & al. 2020). Molecular barcoding has therefore become an important tool in the identification of fungi, as well as other organisms, and is even being implemented in citizen science projects (Geiger & al. 2016;Beenken & al. 2017;Bubner & al. 2019;Chiovitti & al. 2019). ...
DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated
issues with BLAST searches, including the use of pairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leiotrametes), with three new combinations: C. flavidus, C. lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines.
... Thus, we concluded that the Thai Lygodium rust fungus belonged to Milesina. In these analyses, we included LSU sequences of 12 European Milesina species recently published by Bubner et al. (2019). In the study of European Milesina species (Bubner et al. 2019), ITS sequences separated only 4 of 11 species and LSU sequences did not improve resolution of species relationships, even though urediniospore morphology distinguished Milesina species (except for two species). ...
... In these analyses, we included LSU sequences of 12 European Milesina species recently published by Bubner et al. (2019). In the study of European Milesina species (Bubner et al. 2019), ITS sequences separated only 4 of 11 species and LSU sequences did not improve resolution of species relationships, even though urediniospore morphology distinguished Milesina species (except for two species). In their study, Bubner et al. (2019) revealed four distinct phylogenetic groups that correlated with particular patterns in the urediniospore morphology and proposed four sections in Milesina. ...
... In the study of European Milesina species (Bubner et al. 2019), ITS sequences separated only 4 of 11 species and LSU sequences did not improve resolution of species relationships, even though urediniospore morphology distinguished Milesina species (except for two species). In their study, Bubner et al. (2019) revealed four distinct phylogenetic groups that correlated with particular patterns in the urediniospore morphology and proposed four sections in Milesina. Urediniospore morphology and ML or NJ tree recovered from LSU sequence analyses, however, did not support the inclusion of M. thailandica to either one of the four sections that Bubner et al. (2019) proposed. ...
A new rust fungus was found on Lygodium flexuosum at Doi Suthep-Pui National Park in Chiang Mai Province, Thailand. Puccinia lygodii was the only rust fungus currently known on Lygodium spp. (Lygodioideae, Schizaeaceae, Schizaeales) from southern North America through northern South America. The new fungus produced uredinia linearly between veins, causing yellowish streaks, on the abaxial frond surface. The sori were covered with a layer of thin-walled fungal cells beneath the host epidermis and surrounded by thin-walled paraphyses. The sori did not have a distinct central aperture with ostiolar cells but ruptured irregularly to release urediniospores. Urediniospores were obovoid, obovoid-ellipsoid, or pyriform. The wall was thin, colorless, and completely echinulate. Neither amphispores nor teliospores were observed. The sorus and spore morphology indicated the taxonomic affinity of the fungus to the fern rust genera Hyalopsora and Milesina. A molecular phylogenetic analysis using nuclear large subunit ribosomal DNA sequence revealed that the Lygodium rust fungus was grouped in a paraphyletic Milesina clade. From the putative host preference, morphology, and estimated phylogenetic relationships, it was concluded that the fungus was a new species of Milesina.
... Anzahl und Verteilung der Keimporen der Urediniosporen bei Rostpilzen auf Gräsern sind bereits von CUMMINS (1956) als wichtiges Bestimmungs-und Artmerkmal bei Grasrosten erkannt worden. In diesem Beitrag testen wir mit dem Ziel der schnellen Artbestimmung Keimporenmerkmale mit Hilfe eines einfachen lichtmikroskopischen Phasenkontrastverfahrens, das bereits bei anderen Rostpilzgruppen (SCHOLLER et al., 2014, BUBNER et al., 2019 ...
In Mitteleuropa sind auf Weizen (Triticum aestivum) drei Rostpilzarten (Pucciniales) bekannt, nämlich der Schwarzrost (Puccinia graminis), der Gelbrost (P. striiformis) und der Braunrost (P. triticina). Diese Arten sind ökonomisch bedeutend. Um sie zu überwachen, frühzeitig zu erkennen und Ernteeinbußen zu minimieren, ist eine schnelle und korrekte Bestimmung der Pilzarten nötig. Hier wurde eine einfache lichtmikroskopische Methode optimiert und getestet, bei der Keimporenmerkmale der Urediniosporen zur Artdifferenzierung herangezogen werden. Die Methode lässt eine eindeutige Bestimmung zu. Die Ergebnisse werden mit Sequenzanalysemethoden in Bezug auf Bestimmungssicherheit, Zeitaufwand und Materialkosten verglichen.
A new species of rust fungi Nyssopsora toonae discovered on living leaves of Toona sinensis (≡ Cedrela sinensis) from Uttarakhand, India, is described and illustrated. N. cedrelae is also reported on the same host plant, but differs from N. toonae which has a wide range of cells (1-4) and diverse teliospores shapes. Such features are not reported in any other species of the Nyssopsora. In a phylogenetic analyses based on partial 28S large subunit (LSU), 18S smaller subunit (SSU), cytochrome c-oxidase subunit 3 (CO3) and complete internal transcribed spacer (ITS) sequence data, all the Nyssopsora spp. along with N. toonae clustered together and form a separate and independent monophyletic lineage sister to Pucciniaceae in Pucciniales. The new family Nyssopsoraceae is introduced to accommodate this lineage based on the phylogenetic evidence and morphological differences from other known families. Nyssopsoraceae is characterised by its teliospores borne singly on a pedicel, with simple or branched projections all over the surface, composed of 1-4 cells (mostly 3-celled), and diverse shape. The teliospores spherical to subspherical (1-celled), dumbbell (2-celled), linearly arranged to triquetrous (3-celled), or T-shaped to tetrahedron (4-celled). A comparison of the morphological features, host plants and geographical distribution of all validly accepted species of Nyssopsora is provided.
During the research on rust fungi in medicinal plants of Guizhou Province, China, a total of 9 rust fungal species were introduced, including 3 new species (Hamaspora rubi-alceifolii, Nyssopsora altissima, and Phragmidium cymosum), as well as 6 known species (Melampsora laricis-populina, Melampsoridium carpini, Neophysopella ampelopsidis, Nyssopsora koelrezidis, P. rosae-roxburghii, P. tormentillae). Notably, N. ampelopsidis and P. tormentillae were discovered for the first time in China, while M. laricis-populina, Me. carpini, and Ny. koelreuteriae were first documented in Guizhou Province. Morphological observation and molecular phylogenetic analyses of these species with similar taxa were compared to confirm their taxonomic identities, and taxonomic descriptions, illustrations and host species of those rust fungi on medicinal plant are provided.
