Gymnosporangium species on Malus: species delineation, diversity and host alternation

Gymnosporangium mori comb. nov. (Pucciniales) for Caeoma mori (≡ Aecidium mori) inferred from phylogenetic evidence

Caeoma mori (≡ Aecidium mori), known as the mulberry rust which is an anamorphic rust fungus forming only aecidioid uredinia, were found on Morus alba in Ibaraki and Saitama Prefectures, Japan. Molecular phylogenetic analyses using the combined dataset of sequences from 28S and 18S of the nuclear ribosomal RNA gene and Cytochrome-c-oxidase subunit 3 of the mitochondrial DNA revealed that this anamorphic rust fungus was a member of the clade composed of the genus Gymnosporangium. Therefore, a new combination, Gymnosporangium mori is proposed for this species. Additionally, a new combination, G. brucense for Roestelia brucensis is proposed by phylogenetic evidence.

Four new species of Puccinia from herbaceous plants in China

Members of Puccinia (Pucciniaceae, Pucciniales) are known as plant pathogens worldwide, which are characterized by their morphology, host association, and molecular data of various genes. In the present study, 10 specimens of Puccinia were collected from four herbaceous plants (Anaphalis hancockii, Anthriscus sylvestris, Halenia elliptica, and Pilea pumila) in China and identified based on morphology and phylogeny. As a result, 10 samples represent four undescribed species of Puccinia, viz., P. apdensia, P. decidua, P. dermatis, and P. lianchengensis, spp. nov. P. apdensia is characterized by its smooth teliospores with thickened apex. P. decidua represents the first Puccinia species inhabiting the host Anaphalis hancockii and is distinguished from the other Puccinia species by its telia and uredinia surrounded by the epidermis. P. dermatis from Halenia elliptica differs from the other Puccinia species on the host genus Halenia by the telia that have epidermis and teliospores with sparsely irregular granulated protrusions. P. lianchengensis is characterized by its teliospore surface with fishnet ornamentation and urediniospores without prominent caps. All of the new species are described and illustrated in this study.

Rust Fungi on Medicinal Plants in Guizhou Province with Descriptions of Three New Species

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.

Comparative transcriptome analysis of juniper branches infected by Gymnosporangium spp. highlights their different infection strategies associated with cytokinins

BACKGROUND

Gymnosporangium asiaticum and G. yamadae can share Juniperus chinensis as the telial host, but the symptoms are completely different. The infection of G. yamadae causes the enlargement of the phloem and cortex of young branches as a gall, but not for G. asiaticum, suggesting that different molecular interaction mechanisms exist the two Gymnosporangium species with junipers.

RESULTS

Comparative transcriptome analysis was performed to investigate genes regulation of juniper in responses to the infections of G. asiaticum and G. yamadae at different stages. Functional enrichment analysis showed that genes related to transport, catabolism and transcription pathways were up-regulated, while genes related to energy metabolism and photosynthesis were down-regulated in juniper branch tissues after infection with G. asiaticum and G. yamadae. The transcript profiling of G. yamadae-induced gall tissues revealed that more genes involved in photosynthesis, sugar metabolism, plant hormones and defense-related pathways were up-regulated in the vigorous development stage of gall compared to the initial stage, and were eventually repressed overall. Furthermore, the concentration of cytokinins (CKs) in the galls tissue and the telia of G. yamadae was significantly higher than in healthy branch tissues of juniper. As well, tRNA-isopentenyltransferase (tRNA-IPT) was identified in G. yamadae with highly expression levels during the gall development stages.

CONCLUSIONS

In general, our study provided new insights into the host-specific mechanisms by which G. asiaticum and G. yamadae differentially utilize CKs and specific adaptations on juniper during their co-evolution.

Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust

Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.

Applying early divergent characters in higher rank taxonomy of Melampsorineae (Basidiomycota, Pucciniales)

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.

Identification and characterization of two new Gymnosporangium species causing rust on Juniperus rigida in China

A serious Juniperus rigida rust disease was found in Gansu Province, China. The disease incidence is approximately 80-90%. We also found rust disease on both Cotoneaster multiflorus and Sorbus in the same location. Two novel Gymnosporangium species were identified from the infected plants. Based on morphological observations and phylogenetic analyses, we describe the two new taxa as G. gansuense and G. granulatosporum. We also determined their life cycles. Moreover, this study documented a novel aeciospore surface structure with two different surface types on one aeciospore. We describe it here as "granular."

Studies on European rust fungi, Pucciniales: molecular phylogeny, taxonomy, and nomenclature of miscellaneous genera and species in Pucciniastraceae and Coleosporiaceae

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.

Genera of phytopathogenic fungi: GOPHY 4

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. Taxonomic novelties: New genera: Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pteridopassalora C. Nakash. & Crous; New species: Ascochyta flava Qian Chen & L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora vinacea J.R. Úrbez-Torres, D.T. O'Gorman & Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen & Gramaje, Celoporthe foliorum H. Suzuki, Marinc. & M.J. Wingf., Cercospora alyssopsidis M. Bakhshi, Zare & Crous, Dendrostoma elaeocarpi C.M. Tian & Q. Yang, Didymella chlamydospora Qian Chen & L. Cai, Didymella gei Qian Chen & L. Cai, Didymella ligulariae Qian Chen & L. Cai, Didymella qilianensis Qian Chen & L. Cai, Didymella uniseptata Qian Chen & L. Cai, Endothia cerciana W. Wang. & S.F. Chen, Leptosphaerulina miscanthi Qian Chen & L. Cai, Nigrospora covidalis M. Raza, Qian Chen & L. Cai, Nigrospora globospora M. Raza, Qian Chen & L. Cai, Nigrospora philosophiae-doctoris M. Raza, Qian Chen & L. Cai, Phytophthora transitoria I. Milenković, T. Májek & T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora variabilis T. Jung, M. Horta Jung & I. Milenković, Pseudocercospora delonicicola C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora farfugii C. Nakash., I. Araki, & Ai Ito, Pseudocercospora hardenbergiae Crous & C. Nakash., Pseudocercospora kenyirana C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora perrottetiae Crous, C. Nakash. & C.Y. Chen, Pseudocercospora platyceriicola C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora xenopunicae Crous & C. Nakash.; New combinations: Heterophaeomoniella pinifoliorum (Hyang B. Lee et al.) L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pseudocercospora pruni-grayanae (Sawada) C. Nakash. & Motohashi., Pseudocercospora togashiana (K. Ito & Tak. Kobay.) C. Nakash. & Tak. Kobay., Pteridopassalora nephrolepidicola (Crous & R.G. Shivas) C. Nakash. & Crous, Pteridopassalora lygodii (Goh & W.H. Hsieh) C. Nakash. & Crous; Typification: Epitypification: Botrytis infestans Mont., Cercospora abeliae Katsuki, Cercospora ceratoniae Pat. & Trab., Cercospora cladrastidis Jacz., Cercospora cryptomeriicola Sawada, Cercospora dalbergiae S.H. Sun, Cercospora ebulicola W. Yamam., Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora ixorana J.M. Yen & Lim, Cercospora liquidambaricola J.M. Yen, Cercospora pancratii Ellis & Everh., Cercospora pini-densiflorae Hori & Nambu, Cercospora profusa Syd. & P. Syd., Cercospora pyracanthae Katsuki, Cercospora horiana Togashi & Katsuki, Cercospora tabernaemontanae Syd. & P. Syd., Cercospora trinidadensis F. Stevens & Solheim, Melampsora laricis-urbanianae Tak. Matsumoto, Melampsora salicis-cupularis Wang, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora angiopteridis Goh & W.H. Hsieh, Pseudocercospora basitruncata Crous, Pseudocercospora boehmeriigena U. Braun, Pseudocercospora coprosmae U. Braun & C.F. Hill, Pseudocercospora cratevicola C. Nakash. & U. Braun, Pseudocercospora cymbidiicola U. Braun & C.F. Hill, Pseudocercospora dodonaeae Boesew., Pseudocercospora euphorbiacearum U. Braun, Pseudocercospora lygodii Goh & W.H. Hsieh, Pseudocercospora metrosideri U. Braun, Pseudocercospora paraexosporioides C. Nakash. & U. Braun, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous, Septogloeum punctatum Wakef.; Neotypification: Cercospora aleuritis I. Miyake; Lectotypification: Cercospora dalbergiae S.H. Sun, Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora profusa Syd. & P. Syd., Melampsora laricis-urbanianae Tak. Matsumoto, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous. Citation: Chen Q, Bakhshi M, Balci Y, Broders KD, Cheewangkoon R, Chen SF, Fan XL, Gramaje D, Halleen F, Horta Jung M, Jiang N, Jung T, Májek T, Marincowitz S, Milenković T, Mostert L, Nakashima C, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies CFJ, Suhaizan L, Suzuki H, Tian CM, Tomšovský M, Úrbez-Torres JR, Wang W, Wingfield BD, Wingfield MJ, Yang Q, Yang X, Zare R, Zhao P, Groenewald JZ, Cai L, Crous PW (2022). Genera of phytopathogenic fungi: GOPHY 4. Studies in Mycology 101: 417-564. doi: 10.3114/sim.2022.101.06.

First report of cedar-quince rust Gymnosporangium clavipes on fruit of dwarf hawthorn Crataegus uniflora in Florida, USA

The dwarf hawthorn Crataegus uniflora Münchh. (Rosaceae, Maloideae) is a small deciduous tree species native to the central and eastern US and south into northern Mexico. Dwarf hawthorn is drought tolerant and commonly found in disturbed areas (e.g., hedges and roadsides). In May 2021, we observed several individuals of dwarf hawthorn growing on the border of an empty field in the Natural Area Teaching Laboratory at The University of Florida main campus in Gainesville, Alachua County, Florida, USA (N29.633382, W82.368350) that were severely infected by fruit galls with visible, whitish aecia (e-Xtra Fig.1). The affected fruit were collected and transported to the Florida Department of Agriculture and Consumer Services - Division of Plant Industry headquarters in Gainesville for identification (FDACS-DPI, 2021-107788). The conspicuous rust fungus, occurring on the fruit (fructicolous), consisted of tubular aecia (roestelioid), 4 - 5 mm in length × 0.5 mm in diameter, with whitish peridia containing bright orange spores in masses. Aeciospores were semigloboid to globoid, some with an angular side, with bright orange contents, 26 - 31 µm in diameter (n= 20). The wall was densely verrucose, hyaline, 3 - 4 µm wide. Side and wall ornamentation are considered diagnostic features (EPPO Bulletin, 2006). Peridial cells of the aecia were hyaline, angular (pentagonal to hexagonal) to irregular, with a thin, convoluted wall, 41- 57 × 30 - 35 µm (n =10). Aeciospores were detected on blackish, mummified berries five months after the initial collection and aecium disappearance. This persistence demonstrates one of the adaptations allowing the pathogen to remain in a given location (e-Xtra Fig.1). The morphological characteristics are consistent with those of Gymnosporangium clavipes Cooke & Peck (Gymnosporangiaceace, Pucciniaceae, Pucciniomycotina) described by Kern (1973). A voucher was deposited in the DPI Herbarium (PIHG, specimen number 15618). The morphological identification was confirmed by molecular identification: following DNA extraction (DNeasy Plant Pro extraction kit, Qiagen Corporation, Hilden, Germany), we amplified a fragment of the internal transcribed spacer (ITS) and the large subunit (LSU) via PCR using the primer pairs Rust2inv/LR6 and Rust28S/LR5 (OK337508) (Aime, 2006); amplicons were then Sanger sequenced. NCBI megaBlast searches (Chen et al. 2015) of the resulting fungal sequences revealed high identity (ITS and LSU) to two G. clavipes vouchers: NYBG461394 (99.86%, Genbank accession no. MN605691) sequenced in the latest publication addressing species delimitation in Gymnosporangium (Zhao et al., 2020), and PPST 2020-104160 (99.72%, GenBank MW148514): the first report of this rust occurring on Crataegus marshallii Eggleston (McVay et al., 2021), also recently found in Gainesville, Florida. Phylogenetic analyses were carried out in the phylogenetic package RAxMLv8.0.0 (Stamatakis, 2014) (e-Xtra Fig. 2) further supports placement of 2021-107788 within G. clavipes. The heteroecious nature of this rust fungus precludes Koch's postulates. Based on exhaustive reviews of collection indices and literature, a specimen of G. clavipes on C. uniflora exists at the U.S. National Fungus collections (BPI 117783A) collected in Newfield, New Jersey in 1888 (Farr & Rossman, 2022); this rust fungus has a host range of at least 18 other species of Crataegus (Farr and Rossman, 2022; McVay et al., 2021; Zhao et al., 2020). This report represents the first published record of G. clavipes on dwarf hawthorn, and the first report in Florida.