Phyllachora species infecting maize and other grass species throughout the Americas represents a complex of closely related species which vary in their host and geographic range

The genus Phyllachora contains numerous obligate fungal parasites that produce raised, melanized structures called stromata on their plant hosts referred to as tar spot. Members of this genus are known to infect many grass species but generally do not cause significant damage or defoliation, with the exception of P. maydis which has emerged as an important pathogen of maize throughout the Americas, but the origin of this pathogen remains unknown. To date, species designations for Phyllachora have been based on host associations and morphology, and most species are assumed to be host specific. We assessed the sequence diversity of 186 single stroma isolates collected from 16 hosts representing 15 countries. Samples included both herbarium and contemporary strains that covered a temporal range from 1905-2019. These 186 isolates were grouped into 5 distinct species with strong bootstrap support. We found three closely related, but genetically distinct groups of Phyllachora are capable of infecting maize in the United States, we refer to these as the P. maydis species complex. Based on herbarium species, we hypothesize that these three groups in the P. maydis species complex originated from Central America, Mexico and the Caribbean. Although two of these groups were only found on maize, the third and largest group contained contemporary strains found on maize and other grass hosts, as well as herbarium specimens from maize and other grasses that include 10 species of Phyllachora. The herbarium specimens were identified based on morphology and host association, but our sequence data indicates some Phyllachora species are capable of infecting a broad range of host species and there may be significant synonymy in the Phyllachora genus and additional work on species delineation and host specificity should be considered.

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Veterinary Fusarioses within the United States

Journal of Clinical Microbiology ◽

10.1128/jcm.01607-16 ◽

2016 ◽

Vol 54 (11) ◽

pp. 2813-2819 ◽

Cited By ~ 21

Author(s):

Kerry O'Donnell ◽

Deanna A. Sutton ◽

Nathan Wiederhold ◽

Vincent A. R. G. Robert ◽

Pedro W. Crous ◽

...

Keyword(s):

United States ◽

Dna Sequence ◽

Species Complex ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The United States ◽

Content Type ◽

Dna Sequence Data ◽

Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

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Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

Phytopathology ◽

10.1094/phyto-07-15-0155-r ◽

2016 ◽

Vol 106 (4) ◽

pp. 362-371 ◽

Cited By ~ 20

Author(s):

P. Cheng ◽

X. M. Chen ◽

D. R. See

Keyword(s):

Ssr Markers ◽

Stripe Rust ◽

Simple Sequence Repeat ◽

Puccinia Striiformis ◽

The United States ◽

Grass Species ◽

Cereal Crops ◽

Sequence Repeat ◽

Grass Hosts ◽

Simple Sequence

Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.

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Black Choke Disease Caused by an Ephelis sp. on Purple Fountain Grass in Maryland

Plant Disease ◽

10.1094/pd-90-0112a ◽

2006 ◽

Vol 90 (1) ◽

pp. 112-112

Author(s):

E. Lewis Roberts ◽

J. F. White

Keyword(s):

United States ◽

North America ◽

The United States ◽

Maximum Parsimony Analysis ◽

Bootstrap Support ◽

Herbarium Specimens ◽

Dense Layer ◽

Causal Organism ◽

Plant Nursery ◽

Choke Disease

Purple fountain grass (Pennisetum alopecuroides) is indigenous to Asia, prized for its foxtail-like purple flowers, and widely used as an ornamental. During October 1999, black choke disease was found on P. alopecuroides cv. Hameln (L.) Spreng at a plant nursery in Maryland. Disease symptoms include mummification of inflorescences by black conidial stromata, distorted leaf tissue, and a dense layer of white epiphytic mycelium on the adaxial leaves and culms. Stromata were initially white but became black with age. Microscopic analysis of the isolated fungus indicated that the causal organism was an Ephelis sp., American Type Culture Collection No. MYA-3317. The ephelidial conidia developed in sporodochia on stromata and were hyaline, filiform to acicular, and 18 to 21 × 1 μm. Cultures on potato dextrose agar were off-white and 50 mm in diameter after 14 days at 23°C. Analysis of herbarium specimens of several Balansia spp. revealed that the Ephelis sp. isolate bears morphological resemblance to Asian and not American Balansieae. In fact, the infection observed on Pennisetum sp. forms similarly to Ephelis sp. infection on Oryza sativa L. (Asian) that also results in development of stromata on panicles and a mycelial network enclosing the panicles, preventing maturation and expansion. On both plants, the infected inflorescence becomes black with age and appears mummified as pseudosclerotia form. Furthermore, flag leaves and tillers of both plants appear slightly distorted and silver due to the epibiotic mycelia. The causal agent of black choke disease on rice is Ephelis oryzae Syd. (teleomorph = Balansia oryzae-sativae Hashioka). The mature stroma of E. oryzae forms on the inflorescence and is embedded with a layer of ovate perithecia. Immature stromata bear conidiomata that are cupulate to cushion shaped and black, producing hyaline, branched conidiophores that terminate in phialides. Conidia are ephelidial, filiform to acicular, hyaline, and 18 to 22 × 1.5 μm (2). To determine the phylogenetic relationship between other balansioid fungi and the Ephelis sp. isolate, the nuclear ribosomal internal transcribed spacer (ITS1) region was amplified with primers ITS4 and ITS5 (3). Maximum parsimony analysis of the ITS1 sequences showed that the Ephelis sp. infecting P. alopecuroides cv. Hameln grouped (100% bootstrap support) in a clade with Ephelis oryzae, Balansia sclerotica, Balansia andropogonis, and Balansia sp.; all endemic to Asia and tightly groups with the Asian rice pathogen Ephelis oryzae (100% bootstrap support). Further phylogenetic analysis using topological constraints indicated that Ephelis sp. is not appropriately grouped with American balansioid species. Since P. alopecuroides is often imported to North America from Asia (1), it is likely that Ephelis sp. on P. alopecuroides is endemic to Asia and perhaps was transported along with its host to North America. The disease ontogeny, morphology, and sequence similarities between the Ephelis sp. isolated from Pennisetum sp. and E. oryzae suggests that these fungi are evolutionarily close, sibling species, or conspecific. To our knowledge, this is the first report of choke disease on P. alopecuroides in the United States. References: (1) A. S. Hitchcock. Manual of the Grasses of the United States. A. Chase, ed. U.S. Government Print Office, Washington DC, 1951 (2) F. N. Lee and P. S. Gunnell. Udbatta. Page 29 in: Compendium of Rice Diseases. R. K. Webster and P. S. Gunnell, eds. The American Phytopathological Society, St. Paul. MN, 1992. (3) J. F. White Jr. et al. Mycologia 89:408, 1997.

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Phaeosphaeria chinensis sp. nov. (Phaeosphaeriaceae) with an asexual/sexual morph connection from GuangDong Province, China

Phytotaxa ◽

10.11646/phytotaxa.419.1.2 ◽

2019 ◽

Vol 419 (1) ◽

pp. 28-38 ◽

Cited By ~ 1

Author(s):

KE-KE ZHANG ◽

SINANG HONGSANAN ◽

DANUSHKA S. TENNAKOON ◽

SHENG-LI TIAN ◽

NING XIE

Keyword(s):

New Species ◽

Bayesian Inference ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Guangdong Province ◽

Distinct Species ◽

Bootstrap Support ◽

Comprehensive Description ◽

High Bootstrap ◽

Asexual Morphs

Phaeosphaeria chinensis sp. nov. was found on dead leaves, collected from Guangdong Province, China. Morphology of the new species was compared with other Phaeosphaeria species and related genera of Phaeosphaeriaceae. Phylogenetic analyses of combined ITS, LSU, SSU and TEF-1 sequence data based on maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) revealed that P. chinensis as a distinct species within the Phaeosphaeria with high bootstrap support. The comparison of the new species with other Phaeosphaeria species and a comprehensive description and micrographs are provided. The linkage of sexual and asexual morphs of the new species is also showed.

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Worldwide Phylogeography of the Citrus Brown Spot Pathogen, Alternaria alternata

Phytopathology ◽

10.1094/phyto.2002.92.7.794 ◽

2002 ◽

Vol 92 (7) ◽

pp. 794-802 ◽

Cited By ~ 57

Author(s):

T. L. Peever ◽

A. Ibañez ◽

K. Akimitsu ◽

L. W. Timmer

Keyword(s):

United States ◽

South Africa ◽

Alternaria Alternata ◽

Sequence Data ◽

Random Amplified Polymorphic Dna ◽

Disease Incidence ◽

The United States ◽

Brown Spot ◽

Bootstrap Support ◽

Nucleotide Substitutions

Sixty-five isolates of Alternaria alternata were sampled from brown spot lesions on tangerines and mandarins (Citrus reticulata) and tangerine × grapefruit (C. reticulata × C. paradisi) hybrids in the United States, Colombia, Australia, Turkey, South Africa, and Israel to investigate the worldwide phylogeography of the fungus. Genetic variation was scored at 15 putative random amplified polymorphic DNA (RAPD) loci and 465 bp of an endo-polygalacturonase (endo-PG) gene was sequenced for each isolate. Cluster analysis of RAPD genotypes revealed significant differentiation between United State and Colombia isolates and Turkey, South Africa, Israel, and Australia isolates. Sequencing of endo-PG revealed 21 variable sites when the outgroup A. gaisen (AK-toxin-producing pathogen of Japanese pear) was included and 13 variable sites among the sampled isolates. Nucleotide substitutions at 10 of 13 variable sites represented silent mutations when endo-PG was translated in frame. Eight distinct endo-PG haplotypes were found among the sampled isolates and estimation of a phylogeny with endo-PG sequence data revealed three clades, each with strong bootstrap support. The most basal clade (clade 1) was inferred based on its similarity to the outgroup A. gaisen and consisted exclusively of pathogenic isolates from the United States and Colombia. Clade 2 consisted of pathogenic and nonpathogenic isolates from the United States, Australia, South Africa, and Israel and clade 3 contained pathogenic and nonpathogenic isolates from Australia, South Africa, Israel, and Turkey. Quantitative estimates of virulence (disease incidence) were obtained for isolates from the United States, Colombia, South Africa, Israel, and Turkey by spray inoculating detached citrus leaves and counting the number of lesions 24 h after inoculation. Large differences in virulence were detected among isolates within each location and isolates from the United States were significantly more virulent than isolates from other locations. Several isolates from Colombia, South Africa, Israel, and Turkey had low virulence and 8% of all isolates were nonpathogenic. All but one of the nonpathogenic isolates were found in clade 2 of the endo-PG phylogeny, which also included the most highly virulent isolates sampled.

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A new species of Colletotrichum from Sonchus sp. in Italy

Phytotaxa ◽

10.11646/phytotaxa.314.1.3 ◽

2017 ◽

Vol 314 (1) ◽

pp. 55 ◽

Cited By ~ 4

Author(s):

RUVISHIKA S. JAYAWARDENA ◽

ERIO CAMPORESI ◽

ABDALLAH M. ELGORBAN ◽

ALI H. BAHKALI ◽

JIYE YAN ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Species Complex ◽

Sequence Data ◽

Distinct Species ◽

First Record ◽

Molecular Data ◽

Colletotrichum Species ◽

Morphological And Molecular Data ◽

A New Species

Colletotrichum sonchicola, sp. nov. from Sonchus sp. (dandelion tribe) in Forlì-Cesena Province, Italy, is introduced using morphological and molecular data. Combined phylogenetic analysis of ITS, GAPDH, CHS, ACT and TUB2 sequence data demonstrate that C. sonchicola is a distinct species within the dematium species complex. The new species is illustrated and compared with related taxa. This provides the first record of a Colletotrichum species from the genus Sonchus.

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Morphometric study of Euchiton traversii complex (Gnaphalieae: Asteraceae)

Australian Systematic Botany ◽

10.1071/sb08005 ◽

2008 ◽

Vol 21 (3) ◽

pp. 178 ◽

Cited By ~ 4

Author(s):

Christina Flann ◽

Ilse Breitwieser ◽

Josephine M. Ward ◽

Neville G. Walsh ◽

Pauline Y. Ladiges

Keyword(s):

New Zealand ◽

Species Complex ◽

Distinct Species ◽

Morphometric Study ◽

Herbarium Specimens ◽

Phenetic Analysis ◽

South Eastern ◽

Alpine Regions ◽

Eastern Australia ◽

South Eastern Australia

A morphometric study was undertaken into alpine and subalpine species of Euchiton Cass. (Gnaphalieae: Asteraceae) in the Euchiton traversii species complex in south-eastern Australia and New Zealand. Phenetic analysis of both field-collected and herbarium specimens resolved the following six taxa included: Euchiton traversii (Hook.f.) Holub, Euchiton argentifolius (N.A.Wakef.) Anderb., Euchiton lateralis (C.J.Webb) Breitw. & J.M.Ward, Argyrotegium mackayi (Buchanan) J.M.Ward & Breitw., Argyrotegium fordianum (M.Gray) J.M.Ward & Breitw. and Argyrotegium poliochlorum (N.G.Walsh) J.M.Ward & Breitw. The results support the segregation of the genus Argyrotegium J.M.Ward & Breitw. from Euchiton. E. argentifolius is distinct from E. traversii, but conspecific with A. mackayi. E. lateralis is present in Tasmania as well as New Zealand. The distribution of Australian E. traversii is redefined to mainland alpine regions with a few rare occurrences in Tasmania. Australian E. traversii was shown to be similar to its New Zealand counterparts. Differences between E. lateralis and E. traversii were clarified. A. fordianum and A. poliochlorum are distinct species and their transfer to Argyrotegium is supported.

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Genome-wide and cuticular hydrocarbon evidence shed light on potential drivers of speciation in a Neotropical ant species complex

10.22541/au.163421334.49704543/v1 ◽

2021 ◽

Author(s):

Rubi Meza-Lázaro ◽

Kenzy Peña-Carrillo ◽

Chantal Poteaux ◽

Maria Lorenzi ◽

James Wetterer ◽

...

Keyword(s):

Species Complex ◽

Sequence Data ◽

Cuticular Hydrocarbon ◽

Distinct Species ◽

Species Limits ◽

Geographic Barriers ◽

Genome Wide ◽

Mtdna Sequence ◽

Mating Signal ◽

Southeast Mexico

Reproductive isolation between geographically separated populations is generally considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence and mitonuclear conflict. Here we performed an integrative study based on two genome-wide techniques, 3RAD and ultraconserved elements, coupled with cuticular hydrocarbon and mtDNA sequence data, to assess the species limits within the E. ruidum species-complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex, two widely distributed along the Neotropics and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, cuticular hydrocarbon differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.

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Squalus clarkae sp. nov., a new dogfish shark from the Northwest Atlantic and Gulf of Mexico, with comments on the Squalus mitsukurii species complex

Zootaxa ◽

10.11646/zootaxa.4444.2.1 ◽

2018 ◽

Vol 4444 (2) ◽

pp. 101 ◽

Cited By ~ 5

Author(s):

MARIAH O. PFLEGER ◽

R. DEAN GRUBBS ◽

CHARLES F. COTTON ◽

TOBY S. DALY-ENGEL

Keyword(s):

Gulf Of Mexico ◽

Deep Water ◽

Species Complex ◽

Taxonomic Revision ◽

Distinct Species ◽

Bootstrap Support ◽

Interorbital Space ◽

Low Genetic Diversity ◽

Dogfish Shark ◽

Reproductive Rates

Sharks of the genus Squalus have slow reproductive rates coupled with low genetic diversity, as is typical of deep-water sharks, making this group slow to rebound from depletion due to overfishing. The number of species within Squalus has been expanding recently due to increased attention on taxonomic revision, and a growing research focus on little-known deep-water sharks in general. Here we use genetics and morphology to describe a new species of dogfish shark, Squalus clarkae sp. nov. from the Gulf of Mexico (GoM) which replaces Squalus mitsukurii in this region, and place it in the context of congeners from the Atlantic and elsewhere. Previously, S. clarkae sp. nov. was considered a part of the Squalus mitsukurii species complex, a group of closely related but distinct species. We sequenced the mitochondrial cytochrome oxidase I and the NADH Dehydrogenase II gene of S. mitsukurii from the type location in Japan, S. clarkae sp. nov. from the GoM, as well as three closely related species (S. cubensis, S. blainville, and S. megalops) and S. cf. mitsukurii from Brazil. Squalus clarkae sp. nov. is genetically distinct from other species with significant statistical support (>98.6% bootstrap support/posterior probability), and 2.8% divergent from S. mitsukurii in the type location of Japan. Morphological estimates also revealed differences between S. clarkae sp. nov., S. mitsukurii, and other Atlantic Squalus species, with S. clarkae sp. nov. exhibiting a longer body, smaller interorbital space, shorter caudal fin, and a differently-proportioned first dorsal fin. In general, dogfish sharks in the Atlantic and GoM are characterized by similar but distinct morphology, significant genetic variation, and small species ranges.

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Molecular taxonomy reveals the sexual morph of Nodulosphaeria digitalis in Phaeosphaeriaceae from Campanula trachelium in Italy

Phytotaxa ◽

10.11646/phytotaxa.400.1.1 ◽

2019 ◽

Vol 400 (1) ◽

pp. 1 ◽

Cited By ~ 1

Author(s):

NAPALAI CHAIWAN ◽

DHANUSHKA NADEESHAN WANASINGHE ◽

ERIO CAMPORESI ◽

SAOWALUCK TIBPROMMA ◽

SARANYAPHAT BOONMEE ◽

...

Keyword(s):

Sequence Data ◽

Molecular Taxonomy ◽

First Record ◽

Bootstrap Support ◽

The Novel ◽

Dna Sequence Data ◽

Sexual Morph ◽

The Family ◽

Strong Bootstrap Support ◽

Fungal Genus

The fungal genus Nodulosphaeria is one of the oldest phaeosphaeriaceous genera that comprises saprobic, endophytic and pathogenic species associated with a wide variety of substrates. There are 71 species epithets listed under Nodulosphaeria in Index Fungorum and most of these published records lack illustrations and descriptions, or DNA sequence data and thus it is challenging to confirm their names or investigate taxonomic relationships. In this study, we report the sexual morph of Nodulosphaeria digitalis, a terrestrial saprobe belonging to the genus Nodulosphaeria (Phaeosphaeriaceae, Pleosporales), on stems of Campanula trachelium from Arezzo Province, Italy. This is the first record of a Nodulosphaeria taxon on Campanulaceae. Maximum likelihood, Maximum parsimony and Bayesian inference analyses of combined ITS, LSU, SSU and TEF1-α sequence data reveal that the novel isolate belongs to the family Phaeosphaeriaceae and nests with Nodulosphaeria digitalis with strong bootstrap support. The detailed descriptions and illustrations of the sexual morph of N. digitalis, an updated phylogenetic tree for the genus Nodulosphaeria are provided.

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