First European records of Puccinia modiolae and P. platyspora, two native South American rust fungi, and new observations on their life cycle and morphology.

This paper reports the South American rust fungi Puccinia modiolae and P. platyspora (Pucciniales/Uredinales) as new alien species of the European rust funga. Puccinia modiolae is presently known from Switzerland and Germany, P. platyspora from Switzerland, Germany, and France. The records of P. platyspora are the first ones from outside South America. The specimens were identified by teliospore characters and sequences of the nuclear ribosomal DNA (internal transcribed spacer 2 and domains D1-D2 of the nuclear ribosomal large subunit) and the mitochondrial CO3 (cytochrome c oxidase III) gene. Puccinia modiolae and P. platyspora have been recorded so far in Europe on members of the genera Alcea, predominantly on Alcea rosea, Althaea, and Malva of the Malvaceae, subfam. Malvoideae. Alcea rosea is host of both species and shared also with the common mallow rust, P. malvacearum, allowing for mixed infections. The plant is commonly grown as an ornamental and may play a major role for the spread of the alien Malvaceae rust fungi. It was observed for the first time that P. platyspora can produce spermogonia and aecidium-type aecia, suggesting phenotypic plasticity regarding the formation of spore states. The observed spermogonia mainly remained closed and did not liberate spermatia. They produced telio- and aeciospores besides spermatia in their cavity and eventually converted entirely into telia or, rarely, into aecidium-like sori. Small clusters of aeciospores and peridial cells were commonly found hidden in the telial plectenchyma, and well-developed aecidium-type aecia provided with a peridium developed rarely in the center of mature telia. Spermogonia belonging to group V type 4 were found in P. malvacearum, which is generally supposed to lack spermogonia. Some spermogonia produced only spermatia in their cavity; others formed spermatia and teliospores, and some eventually converted into telia.

Phylogeny, biogeography, and host range of gall midges (Diptera: Cecidomyiidae) feeding on spores of rust fungi (Basidiomycota: Pucciniales).

Rust fungi (Pucciniales) are plant pathogens that can cause devastating yield losses to economically important crops and threaten native plants with extinction. Rusts are usually controlled with fungicides when rust-resistant plant varieties are unavailable. However, natural enemies may offer an alternative to chemicals by acting as biological controls. The larvae of Mycodiplosis Rübsaamen (49 spp.) feed on the spores of rusts and powdery mildew fungi and have been suggested as a potential biocontrol candidate for disease-causing rusts. However, little is known about the phylogenetic relationships, biogeography, and host range of this genus. We screened 5,665 rust specimens from fungarium specimens and field collections and recovered a total of 363 larvae on 315 rust specimens from 17 countries. Three mitochondrial and 2 nuclear loci were amplified and sequenced for the phylogenetic reconstruction of 129 individuals. We recovered 12 clades, of which 12 and 10 were supported with maximum likelihood and Bayesian inference, respectively. Of the 12 clades, 7 comprised species from multiple continents and climatic regions, and 5 comprised species from a single region. Individuals forming clades were collected from 2 to 18 rust species, suggesting that Mycodiplosis species have a broad host range. In total, Mycodiplosis larvae were identified on 44 different rust species collected from 18 plant families. Future studies should focus on expanding field sampling efforts, including data from additional gene regions, and incorporating morphological data to further elucidate species diversity and distribution patterns.

Characterization of the fungal genus Sphaerellopsis associated with rust fungi: species diversity, host-specificity, biogeography, and in-vitro mycoparasitic events of S. macroconidialis on the southern corn rust, Puccinia polysora.

Sphaerellopsis species are putative hyperparasites of rust fungi and may be promising biological control agents (BCA) of rust diseases. However, few detailed studies limit potential BCA development in Sphaerellopsis. Here, we explored the biogeography, host-specificity, and species diversity of Sphaerellopsis and examined the early infection stage of one species, S. macroconidialis, to infer its trophic status. We randomly screened 5,621 rust specimens spanning 99 genera at the Arthur Fungarium for the presence of Sphaerellopsis. We identified 199 rust specimens infected with Sphaerellopsis species on which we conducted morphological and multi-locus phylogenetic analyses. Five Sphaerellopsis species were recovered, infecting a total of 122 rust species in 18 genera from 34 countries. Sphaerellopsis melampsorinearum sp. nov. is described as a new species based on molecular phylogenetic data and morphological features of the sexual and asexual morphs. Sphaerellopsis paraphysata was the most commonly encountered species, found on 77 rust specimens, followed by Sphaerellopsis macroconidialis on 56 and S. melampsorinearum on 55 examined specimens. The type species, Sphaerellopsis filum, was found on 12 rust specimens and Sphaerellopsis hakeae on a single specimen. We also recovered and documented for the first time, the sexual morph of S. macroconidialis, from a specimen collected in Brazil. Our data indicate that Sphaerellopsis species are not host specific and furthermore that most species are cosmopolitan in distribution. However, S. paraphysata is more abundant in the tropics, and S. hakeae may be restricted to Australia. Finally, we confirm the mycoparasitic strategy of S. macroconidialis through in-vitro interaction tests with the urediniospores of Puccinia polysora. Shortly after germination, hyphae of S. macroconidialis began growing along the germ tubes of P. polysora and coiling around them. After 12 days of co-cultivation, turgor loss was evident in the germ tubes of P. polysora, and appressorium-like structures had formed on urediniospores. The interaction studies indicate that Sphaerellopsis species may be more effective as a BCA during the initial stages of rust establishment.

Phylogenetics of the rust fungi (Pucciniales) of South Africa, with notes on their life histories and possible origins.

South Africa has an indigenous rust (Pucciniales) funga of approximately 460 species. This funga was sampled with species from as many genera as possible. The nuclear ribosomal large subunit (28S) region was amplified from samples representing 110 indigenous species, as well as the small subunit (18S) region and the cytochrome c oxidase subunit 3 (CO3) in some cases, and these were used in phylogenetic analyses. One new species is described, 12 new combinations made, six names reinstated, and two life history connections made. The life histories of this funga were summarized; it is dominated by species with contracted life histories. The majority of species are autoecious, with a small proportion being heteroecious. Of the autoecious species, many will likely be homothallic with no spermagonia. A shortened life history with homothallism allows for a single basidiospore infection to initiate a local population buildup under the prevailing unpredictable climatic conditions. Suggestions are made as to the possible origin of this funga based on the development of the modern South African flora. It is postulated that the rusts of South Africa are of relatively recent origin, consisting of three groups. Firstly, there is an African tropical element with members of the Mikronegerineae (Hemileia), the Sphaerophragmiaceae (Puccorchidium, Sphaerophragmium), and certain Uredinineae (Stomatisora). Their immediate ancestors likely occurred in the tropical forests of Africa during the Paleogene. Secondly, there is a pantropical element including the Raveneliaceae (e.g., Diorchidium, Maravalia, Ravenelia sensu lato, Uropyxis). This likely diversified during the Neogene, when the mimosoids became the dominant trees of the developing savannas. Thirdly, the Pucciniaceae invaded Africa as this continent pushed northward closing the Tethys Sea. They diversified with the development of the savannas as these become the dominant habitat in most of Africa, and are by far the largest component of the South African rust funga.

Rust HUBB: DNA barcode-based identification of Pucciniales.

Rust fungi (Pucciniales, Basidiomycota) are a species-rich (ca. 8000 species), globally distributed order of obligate plant pathogens. Rust species are host-specific, and as a group they cause disease on many of our most economically and/or ecologically significant plants. As such, the ability to accurately and rapidly identify these fungi is of particular interest to mycologists, botanists, agricultural scientists, farmers, quarantine officials, and associated stakeholders. However, the complexities of the rust life cycle, which may include production of up to five different spore types and alternation between two unrelated host species, have made standard identifications, especially of less-documented spore states or alternate hosts, extremely difficult. The Arthur Fungarium (PUR) at Purdue University is home to one of the most comprehensive collections of rust fungi in the world. Using material vouchered in PUR supplemented with fresh collections we generated DNA barcodes of the 28S ribosomal repeat from > 3700 rust fungal specimens. Barcoded material spans 120 genera and > 1100 species, most represented by several replicate sequences. Barcodes and associated metadata are hosted in a publicly accessible, BLAST searchable database called Rust HUBB (Herbarium-based Universal Barcode Blast) and will be continuously updated.

A higher-rank classification for rust fungi, with notes on genera.

The rust fungi (Pucciniales) with 7000+ species comprise one of the largest orders of Fungi, and one for which taxonomy at all ranks remains problematic. Here we provide a taxonomic framework, based on 16 years of sampling that includes ca. 80 % of accepted genera including type species wherever possible, and three DNA loci used to resolve the deeper nodes of the rust fungus tree of life. Pucciniales are comprised of seven suborders - Araucariomycetineae subord. nov., Melampsorineae, Mikronegeriineae, Raveneliineae subord. nov., Rogerpetersoniineae subord. nov., Skierkineae subord. nov., and Uredinineae - and 18 families - Araucariomycetaceae fam. nov., Coleosporiaceae, Crossopsoraceae fam. nov., Gymnosporangiaceae, Melampsoraceae, Milesinaceae fam. nov., Ochropsoraceae fam. & stat. nov., Phakopsoraceae, Phragmidiaceae, Pileolariaceae, Pucciniaceae, Pucciniastraceae, Raveneliaceae, Rogerpetersoniaceae fam. nov., Skierkaceae fam. & stat. nov., Sphaerophragmiaceae, Tranzscheliaceae fam. & stat. nov., and Zaghouaniaceae. The new genera Araucariomyces (for Aecidium fragiforme and Ae. balansae), Neoolivea (for Olivea tectonae), Rogerpetersonia (for Caeoma torreyae), and Rossmanomyces (for Chrysomyxa monesis, Ch. pryrolae, and Ch. ramischiae) are proposed. Twenty-one new combinations and one new name are introduced for: Angiopsora apoda, Angiopsora chusqueae, Angiopsora paspalicola, Araucariomyces balansae, Araucariomyces fragiformis, Cephalotelium evansii, Cephalotelium neocaledoniense, Cephalotelium xanthophloeae, Ceropsora weirii, Gymnotelium speciosum, Lipocystis acaciae-pennatulae, Neoolivea tectonae, Neophysopella kraunhiae, Phakopsora pipturi, Rogerpetersonia torreyae, Rossmanomyces monesis, Rossmanomyces pryrolae, Rossmanomyces ramischiae, Thekopsora americana, Thekopsora potentillae, Thekopsora pseudoagrimoniae, and Zaghouania notelaeae. Higher ranks are newly defined with consideration of morphology, host range and life cycle. Finally, we discuss the evolutionary and diversification trends within Pucciniales. Citation: Aime MC, McTaggart AR (2020). A higher-rank classification for rust fungi, with notes on genera. Fungal Systematics and Evolution 7: 21-47. doi: 10.3114/fuse.2021.07.02.

Host Adaptation and Virulence in Heteroecious Rust Fungi.

Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.

Variation in the Internal Transcribed Spacer Region of Phakopsora pachyrhizi and Implications for Molecular Diagnostic Assays.

Phakopsora pachyrhizi, the causal agent of soybean rust (SBR), is a global threat to soybean production. Since the discovery of SBR in the continental United States, quantitative polymerase chain reaction assays based on the internal transcribed spacer (ITS) ribosomal DNA locus were established for its rapid detection. However, insufficient data were initially available to test assays against factors that could give rise to misidentification. This study aimed to reevaluate current assays for (i) the potential for false-positive detection caused by nontarget Phakopsora species and (ii) the potential for false-negative detection caused by intraspecific variation within the ITS locus of P. pachyrhizi. A large amount of intraspecific and intragenomic variation in ITS was detected, including the presence of polymorphic ITS copies within single leaf samples and within single rust sori. The diagnostic assays were not affected by polymorphisms in the ITS region; however, current assays are at risk of false positives when screened against other species of Phakopsora. This study raises caveats to the use of multicopy genes (e.g., ITS) in single-gene detection assays and discusses the pitfalls of inferences concerning the aerobiological pathways of disease spread made in the absence of an evaluation of intragenomic ITS heterogeneity.

The new species Puccinia telimutans causes Mexican potato rust disease of wild potatoes and shows a unique telial metamorphosis.

Puccinia telimutans is described as a new species of rust fungi (Basidiomycota, Pucciniales) and causal agent of Mexican potato rust disease of the endemic wild potatoes Solanum demissum and S. verrucosum from Mexico. It is microcyclic and produces telia that show a unique succession of one-celled, catenulate teliospores that germinate upon maturity, followed by resting teliospores that are pedicellate and two-celled. Puccinia telimutans appears to be restricted to Mexico and has formerly been confused with P. pittieriana, which causes common potato rust in South America.

Pucciniamodiolae in North America: distribution and natural host range.

Pucciniamodiolae, a rust fungus pathogen of Carolina bristlemallow, Modiolacaroliniana (Malvaceae), is newly reported from North America, appears to be well established along the Gulf coast and is likely to have been introduced from South America. Its taxonomy, distribution and natural host range are discussed and a lectotype designated for this species. Malvasylvestris and Alcearosea are reported as new hosts for the rust. Additional new records for Malvaceae rusts are made for P.modiolae on Alcearosea from Brazil, P.heterospora on Herissantiacrispa in Florida and P.heterogenea on Malva sp. in Peru. Finally, an identification key for the microcyclic Puccinia species on members of Malvaceae in North America is provided.

The species of Coleosporium (Pucciniales) on Solidago in North America.

Species of Coleosporium (Pucciniales) are rust fungi that typically alternate between pines and angiosperms. In North America, species of Coleosporium often infect Solidago (goldenrods), although their taxonomy on these hosts is unresolved. Joseph. C. Arthur and George B. Cummins regarded these as a single species, Coleosporium solidaginis (fide Arthur) or C. asterum (fide Cummins), but later inoculation studies demonstrated the presence of more than one species, distinguishable by their aecial hosts. A more recent taxonomic study of Coleosporium found that specimens on Solidago identified as C. asterum in North America were not conspecific with the type, which is from Japan, prompting the present study. Herein, we conducted a systematic study on ca. 60 collections of Coleosporium infecting species of Asteraceae from North America using regions of ribosomal DNA and morphology of teliospores and basidia. Our data indicate at least three species of Coleosporium occur on Solidago in North America, C. solidaginis, C. montanum comb. nov., which is proposed for the taxon that has commonly been identified as C. asterum in North America, and C. delicatulum, all of which can be differentiated by morphology of their basidia. In addition, the challenges of marker selection for molecular barcoding of rust fungi is discussed.

Deconstructing the evolutionary complexity between rust fungi (Pucciniales) and their plant hosts.

The rust fungi (Pucciniales) are the most speciose natural group of plant pathogens, members of which possess the most complex lifecycles in Fungi. How natural selection works on the Pucciniales has been the subject of several hypotheses in mycology. This study uses molecular age estimation using sequence data from multiple loci, and cophylogeny reconciliation analyses to test hypotheses regarding how the aecial and telial stages in the lifecycle of rust fungi may have differentially impacted their diversification. Molecular age estimates show that the timing of diversification in the Pucciniales correlates with the diversification of their gymnosperm and angiosperm hosts. Host reconciliation analyses suggest that systematic relationships of hosts from the aecial stage of the Pucciniales lifecycle better reflect the systematic relationships among the Pucciniales. The results demonstrate the relative importance of this stage on the overall evolution of the Pucciniales and supports hypotheses made by Leppik over half a century ago. This study represents the first evaluation of how different life stages in the Pucciniales shape the evolution of these fungi.

Phylogenetics and Phylogenomics of Rust Fungi.

Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi. In this chapter, we provide an overview of the current status and special challenges of rust genomics, and we highlight how phylogenomics may provide new perspectives and answer long-standing questions regarding the biology of rust fungi.

Host jumps shaped the diversity of extant rust fungi (Pucciniales).

The aim of this study was to determine the evolutionary time line for rust fungi and date key speciation events using a molecular clock. Evidence is provided that supports a contemporary view for a recent origin of rust fungi, with a common ancestor on a flowering plant. Divergence times for > 20 genera of rust fungi were studied with Bayesian evolutionary analyses. A relaxed molecular clock was applied to ribosomal and mitochondrial genes, calibrated against estimated divergence times for the hosts of rust fungi, such as Acacia (Fabaceae), angiosperms and the cupressophytes. Results showed that rust fungi shared a most recent common ancestor with a mean age between 113 and 115 million yr. This dates rust fungi to the Cretaceous period, which is much younger than previous estimations. Host jumps, whether taxonomically large or between host genera in the same family, most probably shaped the diversity of rust genera. Likewise, species diversified by host shifts (through coevolution) or via subsequent host jumps. This is in contrast to strict coevolution with their hosts. Puccinia psidii was recovered in Sphaerophragmiaceae, a family distinct from Raveneliaceae, which were regarded as confamilial in previous studies.

A co-evolutionary relationship exists between Endoraecium (Pucciniales) and its Acacia hosts in Australia.

Endoraecium is a genus of rust fungi that infects several species of Acacia in Australia, South-East Asia and Hawaii. This study investigated the systematics of Endoraecium from 55 specimens in Australia based on a combined morphological and molecular approach. Phylogenetic analyses were conducted on partitioned datasets of loci from ribosomal and mitochondrial DNA. The recovered molecular phylogeny supported a recently published taxonomy based on morphology and host range that divided Endoraecium digitatum into five species. Spore morphology is synapomorphic and there is evidence Endoraecium co-evolved with its Acacia hosts. The broad host ranges of E. digitatum, E. parvum, E. phyllodiorum and E. violae-faustiae are revised in light of this study, and nine new species of Endoraecium are described from Australia based on host taxonomy, morphology and phylogenetic concordance.

Bioprospección de los hiperparásitos cicinobolus cesatii de bary y eudarluca caricis (Biv.) O.E. Erikss sobre cultivos y plantas adyacentes en la región central de Guatemala / Bioprospecting of fungal hyperparasites cicinobolus cesatii de bary and eudarluca caricis (Biv.) O.E. Erikss on crops and adjacent plants in central region of Guatemala

Se realizó una bioprospección para detectar los hiperparásitos Cicinobolus cesatii y Eudarluca caricis en la región central de Guatemala para establecer la presencia y la obtención de cepas prometedoras para control biológico. Setecientos seis muestras de plantas silvestres y cultivadas fueron analizadas, en 16 se detectó C. cesatii y en 46 E. caricis. Las regiones con más detecciones de ambos hiperparásitos fueron San Juan Comalapa y Tecpán Guatemala del departamento de Chimaltenango, emergiendo como una región con alto potencial biológico y variabilidad. Se obtuvieron aislamientos e hicieron comparaciones de estructuras reproductivas y se estableció que existe variabilidad a través de análisis estadístico que marcó diferencias significativas al 5% de significancia al comparar entre cepas de la misma localidad y entre localidades, además de la diferencia entre origen vegetal. También se estableció que hay cepas promisorias de C. cesatii aislado de Physalis sp. y E. caricis aislado de Prunus sp., Zea mays y Phaseolus vulgaris. El estudio pone de manifiesto el potencial de presencia de ambos agentes sobre plantas silvestres o áreas sin aplicación de fungicidas.

Bioprospecting was performed to detect hyperparasites Cicinobolus cesatii and Eudarluca caricis in central region of Guatemala to establish their presence and obtain promising strains to be use in biological control. Seven hundred and six samples from wild and cultivated plants were analyzed; C. cesatii was detected in 16 samples, and 46 cases of E. caricis. Both hyperparasites were identified in San Juan Comalapa and Tecpan of Chimaltenango County, having high biological potential and variability. Reproductive structures comparison of the different isolates was made and its variability was established through statistical analysis showing significant differences when they were compare between strains from the same site and between sites, also they showed difference between plant origins. These strains such as C. cesatii from Physalis sp. and E. caricis from Prunus sp., Zea mays and Phaseolus vulgaris have a high potential. This research showed a high presence of both agents on wild plants or areas without application of fungicides.

Online identification guides for Australian smut fungi (Ustilaginomycotina) and rust fungi (Pucciniales).

Interactive identification keys for Australian smut fungi (Ustilaginomycotina and Pucciniomycotina, Microbotryales) and rust fungi (Pucciniomycotina, Pucciniales) are available online at http://collections.daff.qld.gov.au. The keys were built using Lucid software, and facilitate the identification of all known Australian smut fungi (317 species in 37 genera) and 100 rust fungi (from approximately 360 species in 37 genera). The smut and rust keys are illustrated with over 1,600 and 570 images respectively. The keys are designed to assist a wide range of end-users including mycologists, plant health diagnosticians, biosecurity scientists, plant pathologists, and university students. The keys are dynamic and will be regularly updated to include taxonomic changes and incorporate new detections, taxa, distributions and images. Researchers working with Australian smut and rust fungi are encouraged to participate in the on-going development and improvement of these keys.

Calidion bombacis, a new combination for Uredo bombacis with the record of Bombacopsisglabra (Bombacaceae) as a new host from Brazil / Calidion bombacis, uma nova combinação para Uredo bombacis e o relato de Bombacopsisglabra (Bombacaceae), como um novo hospedeiro no Brasil

The new combination Calidion bombacis is proposed for the rust species formerly known as Uredobombacis. This nomenclatural change is based on the examination of newly collected material of this fungus from a new host, Bombacopsisglabra from Brazil, and reexamination of the isotype. Until now this fungus was only known to occur in Asia (China, India and Sri Lanka). Therefore, this is also the first record of this fungus from the Neotropics.

A combinação nova Calidion bombacis é proposta para a ferrugem anteriormente conhecida como Uredo bombacis. Esta modificação nomenclatural é proposta baseada no exame de material deste fungo coletado em um novo hospedeiro, Bombacopsisglabra (Bombacaceae) no Brasil e reexame do isotipo. Até então este fungo tinha sido relatado apenas na Ásia (China, Índia e Sri Lanka). Portanto, este é o primeiro relato deste fungo nos Neotrópicos.

Calidion bombacis, a new combination for Uredo bombacis with the record of Bombacopsis glabra (Bombacaceae) as a new host from Brazil.

The new combination Calidion bombacis is proposed for the rust species formerly known as Uredo bombacis. This nomenclatural change is based on the examination of newly collected material of this fungus from a new host, Bombacopsis glabra from Brazil, and reexamination of the isotype. Until now this fungus was only known to occur in Asia (China, India and Sri Lanka). Therefore, this is also the first record of this fungus from the Neotropics.