Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

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.

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.

Isolation and identification of Tussilago farfara leaf spot caused by Alternaria alternata in China

Tussilago farfara is of vital medical value. A new leaf spot disease was observed on T. farfara leaves, in Dingxi, Gansu Province, China, in October 2019. In order to research the pathogen, the diseased samples were collected for isolation and identification. The isolate KD3 was verified by pathogenicity test, as the pathogen causing the T. farfara leaf spot disease. Its morphological characteristics were consistent with Alternaria alternata, the colony color gray-green with concentric rings, conidia fusiform and pear-shaped, brown, with 1-7 septa and 0-3 longitudinal septa, conidia size (19. 62-44.49) μm × (6.97-10.53) μm, beak length (1.35-10.03) μm × (1.01-3.63) μm, and the spore phenotype was a dwarf tree-like chain of short conidia. Multilocus sequences analysis manifested that the internal transcribed spacer (ITS), Alternaria major allergen (Alta1), and Calcium barine (CAL) sequences of strain KD3 were most closely to A. alternata (A23), with the homology of 99.47%, 99.56% and 98.28%, respectively. Based on morphological and molecular characteristics, strain KD3 was identified as A. alternata. OA was the optimal medium for its growth and PCA medium was the optimal for sporulation. This is the first report of A. alternata causing T. farfara leaf spots in China.

Taxonomic investigation of selected rust fungi using scanning electron microscopy from Khyber Pakhtunkhwa, Pakistan

Rusts comprises the largest natural group of plant pathogens including approximately 8% of all described Fungi. Rust fungi are extremely plant pathogens responsible for great losses to agriculture productivity. Rust species belong to several genera among which more than half are Puccinia species. In Pakistan, rust causes severe damage to agriculture crops. Current study was carried out to identify and characterize different rust species common in the research area through microscopy and Scanning electron microscopy (SEM) in Khyber Pakhtunkhwa, Pakistan. Morpho-anatomical investigation of each collected rust species was carried out using different standard protocols. The dimensions of spores were measured and snapped under a stereomicroscope. SEM was used to examine the shape, size, and ornamentation of the spores of each rust fungus. Results revealed documentation of seven rust fungi, that is, Melampsora euphorbiae, Phragmidium barclayi, Puccinia nepalensis, P. exhausta, P. menthae, Uromyces capitatus, and Uromyces decorates belong to four different genera, were recorded. SEM revealed that spermogonia and Aecia were missing in most of the rust fungus studied. Uredinia was found in a scattered, irregular, lengthy, and epidermis-enclosed form. Urediniospores were found to be ovulating, elongated, echinulate, globose to sub-globose, ellipsoid to ovoid, and globose to sub-globose. Telia was found as sub-epidermal, amphigenous, dispersed, minute, and spherical cells. Teliospores ranged in form from cylindrical to oblong. The germ pores were detected in both apical (top cell) and basal (bottom cell) idiosyncratic and pedicel-attached cells. The techniques used in the current investigation will aid mycologists in rust identification and microscopic characterization.

Fungal species boundaries in the genomics era

Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.

A Multi-Gene Analysis and Potential Spatial Distribution of Species of the Strodei Subgroup of the Genus Nyssorhynchus (Diptera: Culicidae)

Nyssorhynchus strodei (Root) is an understudied species of potential epidemiological importance, having been found naturally infected in Brazil with Plasmodium falciparum Welch, Plasmodium vivax Grassi & Feletti, and Plasmodium malariae Feletti & Grassi. It belongs to the strodei subgroup that includes Nyssorhynchus albertoi (Unti), Nyssorhynchus arthuri (Unti), Nyssorhynchus rondoni (Neiva & Pinto), Nyssorhynchus striatus (Sant'Ana & Sallum), and three unnamed species, Nyssorhynchus arthuri B, Nyssorhynchus arthuri C, and Nyssorhynchus arthuri D. As the accurate identification of vector species is of fundamental importance for public health entomology, the aim of the study was to provide additional information for the presence of seven species that had been previously misidentified as Ny. strodei. Bayesian phylogenetic analyses using DNA sequences of the genes COI mtDNA, white, CAD and CAT nuclear genes confirmed Ny. albertoi, Ny. arthuri, Ny. strodei, and Ny. striatus as distinct groups within the strodei subgroup and corroborated the presence of three undescribed species under the name Ny. arthuri. Results of the GMYC model analysis corroborated Ny. arthuri B, Ny. arthuri C, and Ny. arthuri D; however, they did not distinguish between Ny. strodei and Ny. albertoi. Predicted distribution of seven species based on maximum entropy in MaxEnt showed that each species has its specific ecological niche suitability.

Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust

Coffee leaf rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hypervirulent strains, the population evolutionary history and potential of this pathogen remain poorly understood. To address this issue, we used restriction site-associated DNA sequencing (RADseq) to generate ∼19 000 single nucleotide polymorphisms (SNPs) across a worldwide collection of 37 Hv samples. Contrary to the long-standing idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism. Using phylogenetic and pathological data, we show that one of these lineages (C3) infects almost exclusively the most economically valuable coffee species (tetraploids that include Coffea arabica and interspecific hybrids), whereas the other lineages (C1 and C2) are severely maladapted to these hosts, but successfully infect diploid coffee species. Population dynamic analyses suggest that the C3 group may be a recent 'domesticated' lineage that emerged via host shift from diploid coffee hosts. We also found evidence of recombination occurring within this group, which could explain the high pace of pathotype emergence despite the low genetic variation. Moreover, genomic footprints of introgression between the C3 and C2 groups were discovered and raise the possibility that virulence factors may be quickly exchanged between groups with different pathogenic abilities. This work advances our understanding of the evolutionary strategies used by plant pathogens in agro-ecosystems with direct and far-reaching implications for disease control.