Genetic and phenotypic characterization of the fungal pathogen Cytospora plurivora from western Colorado peach orchards and the development of a ddPCR assay for detection and quantification

2021 ◽  
Author(s):  
Jane Stewart ◽  
Stephan Miller ◽  
Frida Zink ◽  
Jorge Caballero ◽  
Luke Tembrock
Keyword(s):  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Digital Pcr ◽  
The United States ◽  
Morphological Data ◽  
Phenotypic Characterization ◽  
Ancestral State ◽  
Internal Transcribed Spacer Region ◽  
Western Colorado ◽  
Peach Trees

Cytospora canker is one of the most important diseases affecting peach production in Colorado, yet previous efforts to characterize Cytospora species diversity in Colorado have relied exclusively on morphological traits. Recently, several new Cytospora species were described from peach orchards within the United States using molecular and morphological data, prompting the need to reexamine Cytospora spp. present on peach trees in Colorado. A total of 137 isolates of Cytospora spp. were collected from eight orchards in western Colorado. Isolates were sequenced at the ITS (internal transcribed spacer) region and EF1a (elongation factor 1 alpha) and assessed with reference sequences in phylogenetic analyses. All isolates from western Colorado peach trees resolved with the newly described Cytospora plurivora. In addition to molecular characterization, temperature growth and virulence assays were conducted to assess phenotypic variation among the isolates from western Colorado. Variation across isolates was found both in growth at different temperatures and in virulence. Ancestral state reconstruction analyses resolved the most virulent (and most often collected) haplotypes together in a well-supported clade from which a single monophyletic origin of high virulence can be inferred. Finally, a droplet digital PCR assay was developed for use in ongoing and future studies to detect and quantify C. plurivora from field and laboratory samples.

scholarly journals Phomopsis Stem Canker: A Reemerging Threat to Sunflower (Helianthus annuus) in the United States

2015 ◽  
Vol 105 (7) ◽  
pp. 990-997 ◽  
Author(s):  
Febina M. Mathew ◽  
Kholoud M. Alananbeh ◽  
James G. Jordahl ◽  
Scott M. Meyer ◽  
Lisa A. Castlebury ◽  
...  
Keyword(s):  
United States ◽  
Helianthus Annuus ◽  
Great Plains ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Stem Canker ◽  
The United States ◽  
Northern Great Plains ◽  
Type Specimens ◽  
Internal Transcribed Spacer Region

Phomopsis stem canker causes yield reductions on sunflower (Helianthus annuus L.) on several continents, including Australia, Europe, and North America. In the United States, Phomopsis stem canker incidence has increased 16-fold in the Northern Great Plains between 2001 and 2012. Although Diaporthe helianthi was assumed to be the sole causal agent in the United States, a newly described species, D. gulyae, was found to be the primary cause of Phomopsis stem canker in Australia. To determine the identity of Diaporthe spp. causing Phomopsis stem canker in the Northern Great Plains, 275 infected stems were collected between 2010 and 2012. Phylogenetic analyses of sequences of the ribosomal DNA internal transcribed spacer region, elongation factor subunit 1-α, and actin gene regions of representative isolates, in comparison with those of type specimens, confirmed two species (D. helianthi and D. gulyae) in the United States. Differences in aggressiveness between the two species were determined using the stem-wound method in the greenhouse; overall, D. helianthi and D. gulyae did not vary significantly (P ≤ 0.05) in their aggressiveness at 10 and 14 days after inoculation. These findings indicate that both Diaporthe spp. have emerged as sunflower pathogens in the United States, and have implications on the management of this disease.

Amanita submelleialba sp. nov. in section Amanita from northern Thailand

Phytotaxa ◽  
2021 ◽  
Vol 513 (2) ◽  
pp. 129-140
Author(s):  
YUAN S. LIU ◽  
JIAN-KUI LIU ◽  
PETER E. MORTIMER ◽  
SAISAMORN LUMYONG
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Line Drawing ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Nuclear Rdna ◽  
Internal Transcribed Spacer Region ◽  
Northern Thailand ◽  
Extant Species ◽  
Distinct Lineage

Amanita submelleialba sp. nov. in section Amanita, is described from northern Thailand based on both multi-gene phylogenetic analysis and morphological evidences. It is characterized by having small to medium-sized basidiomata; a yellow to yellowish pale pileus covering pyramidal to subconical, white to yellow white volval remnants; globose stipe base covered conical, white to yellow white volval remnants; fugacious subapical annulus; and absent clamps. Multi-gene phylogenetic analyses based on partial nuclear rDNA internal transcribed spacer region (ITS), partial nuclear rDNA larger subunit region (nrLSU), RNA polymerase II second largest subunit (RPB2), partial translation elongation factor 1-alpha (TEF1-α) and beta-tubulin gene (TUB) indicated that A. submelleialba clustered together with A. elata and A. mira, but represented as a distinct lineage from other extant species in section Amanita. The detailed morphological characteristics, line-drawing illustration and comparisons with morphologically similar taxa are provided.

scholarly journals Identification and Characterization of Botryosphaeria spp. Causing Gummosis of Peach Trees in Hubei Province, Central China

Plant Disease ◽  
2011 ◽  
Vol 95 (11) ◽  
pp. 1378-1384 ◽  
Author(s):  
Fan Wang ◽  
Lina Zhao ◽  
Guohuai Li ◽  
Junbin Huang ◽  
Tom Hsiang
Keyword(s):  
Prunus Persica ◽  
Elongation Factor ◽  
Fruit Trees ◽  
Hubei Province ◽  
Central China ◽  
Internal Transcribed Spacer Region ◽  
Fusicoccum Aesculi ◽  
Peach Trees ◽  
Production Areas ◽  
Genomic Regions

Peach (Prunus persica) is one of the most important and widely grown fruit trees in China; however, perennial gummosis on trunks and branches is a major problem in peach orchards of Hubei Province, one of the most important peach production areas of China. In order to identify the gummosis-causing agents, diseased trunks and branches were collected from 11 peach orchards in Hubei Province. Fungal isolates were obtained from these samples, yielding three species: Botryosphaeria dothidea (anamorph Fusicoccum aesculi), B. rhodina (anamorph Lasiodiplodia theobromae), and B. obtusa (anamorph Diplodia seriata). They were identified based on conidial morphology and cultural characteristics, as well as analyses of nucleotide sequences of three genomic regions: the internal transcribed spacer region, a partial sequence of the β-tubulin gene, and the translation elongation factor 1-α gene. Fusicoccum aesculi was found in all 11 orchards but L. theobromae was found only in Shayang County in the Jingmen region and D. seriata only in Gong'an County in the Jingzhou region. Via artificial inoculation using mycelia on wounded twigs or branches, these three species were all found to be pathogenic, causing dark lesions on the twigs and branches and, sometimes, gum exudation from diseased parts. Isolates of L. theobromae were the most virulent and caused the largest lesions and most copious gummosis, and D. seriata had less gum than the other two species. This report represents the first description of L. theobromae and D. seriata as causal agents of gummosis on peach in China.

scholarly journals Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Vol 285 (1893) ◽  
pp. 20181632 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

scholarly journals First Report of Cytospora punicae Causing Wood Canker and Branch Dieback of Pomegranate (Punica granatum) in the United States

Plant Disease ◽  
2014 ◽  
Vol 98 (6) ◽  
pp. 853-853 ◽  
Author(s):  
F. Peduto Hand ◽  
R. A. Choudhury ◽  
W. D. Gubler
Keyword(s):  
United States ◽  
Elongation Factor ◽  
Punica Granatum ◽  
The United States ◽  
Internal Transcribed Spacer Region ◽  
Intermittent Light ◽  
First Report ◽  
Consensus Sequences ◽  
Vascular Discoloration ◽  
Branch Dieback

Pomegranates (Punica granatum L.) are an expanding industry in the United States with California growing approximately 32,000 acres with a crop value of over $155 million (1). During June and July of 2012, we observed severe limb and branch dieback in pomegranate orchards cv. Wonderful located in Contra Costa, Kings, and Kern counties of California. Disease symptoms included yellowing of leaves, branch and limb dieback, wood lesions, and canker formation. Dark brown Cytospora-like cultures were consistently isolated from active cankers on potato dextrose agar (PDA) amended with 100 mg l−1 tetracycline hydrochloride. Three isolates (UCCE1223, UCCE1233, and UCCE1234) representative of each orchard were sub-cultured onto PDA and incubated at 22°C under fluorescent intermittent light (12 h light, 12 h dark). Fungal colonies had whitish mycelia that turned olive green to dark brown with maturity and formed globose and dark brown pycnidia after 12 days. Conidia were hyaline, aseptate, allantoid, and (4) 4.5 to 5 (6) × (1) 1.5 (2) μm (n = 180). Pycnidia formed in culture measured (250) 350 to 475 (650) μm in diameter (n = 40). Identification of the isolates was confirmed by sequence comparison of the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rDNA and part of the translation elongation factor 1-α gene (EF1-α) with sequences available in GenBank. Consensus sequences of both genes of all isolates showed 99% homology to the species Cytospora punicae Sacc. (2). All sequences were deposited in GenBank (Accession Nos. KJ621684 to 89). Pathogenicity of the isolates was determined by branch inoculation. In December 2012, 3-year-old branches of P. granatum cv. Wonderful were inoculated by placing 5-mm-diameter mycelium plugs from the growing margin of 14-day-old PDA cultures in fresh wounds made with a 5-mm-diameter cork-borer. Eight branches per isolate were inoculated on eight different trees. Eight control branches were inoculated with non-colonized PDA agar plugs. Inoculations were covered with Vaseline and wrapped with Parafilm to retain moisture. Branches were harvested in August 2013 and examined for canker development and the extent of vascular discoloration spreading downward and upward from the inoculation point. Isolations from the edge of discolored tissue were conducted to fulfill Koch's postulates. C. punicae was re-isolated from 100% of the inoculated branches. Total length of vascular discoloration averaged 30.2 mm in branches inoculated with the three C. punicae isolates and 9 mm in the control branches. No fungi were isolated from the slightly discolored tissue of the controls. To our knowledge, this is the first report of C. punicae as a fungal trunk pathogen of pomegranate trees in the United States. References: (1) California County Agricultural Commissioners' Data, 2010 Crop Year. USDA NASS California field office, retrieved from http://www.nass.usda.gov/Statistics_by_State/California/ Publications/AgComm/201010cactb00.pdf , 2011. (2) P. A. Saccardo. Sylloge Fungorum 3:256, 1884.

Diaporthe seed decay of soybean [Glycine max (L.) Merr.] is endemic in the United States, but new fungi are involved

Plant Disease ◽  
2020 ◽  
Author(s):  
Kristina Petrovic ◽  
Demetra Skaltsas ◽  
Lisa Castlebury ◽  
Brian Kontz ◽  
Tom Allen ◽  
...  
Keyword(s):  
United States ◽  
Glycine Max ◽  
Seed Quality ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
The United States ◽  
Post Inoculation ◽  
Seed Decay ◽  
Comprehensive Survey ◽  
Glycine Max L

Diaporthe seed decay can compromise seed quality in soybean [Glycine max (L.) Merr.] in the warm and humid production areas of the United States during crop maturation. In the current study, 45 isolates of Diaporthe were recovered from seed sampled from soybean fields affected by Diaporthe-associated diseases in eight U.S. states in 2017. The isolates obtained belonged to 10 species of Diaporthe based on morphology and phylogenetic analyses of the internal transcribed spacer, the partial translation elongation factor 1-alpha, and beta-tubulin gene sequences. The associated species included D. aspalathi, D. caulivora, D. kongii, D. longicolla, D. sojae, D. ueckerae, D. unshiuensis and three novel fungi, D. bacilloides, D. flavescens and D. insulistroma. One isolate each of the 10 species was examined for pathogenicity on seed of cv. ‘Sava’ under controlled conditions. Seven days post-inoculation, significant differences in the percentages of decayed seeds and seedling necrosis were observed among the isolates and the non-inoculated control (p<0.0001). While the isolates of D. bacilloides, D. longicolla, and D. ueckerae caused significantly greater percentage of decayed seeds (p<0.0001), the isolate of D. aspalathi caused the greatest seedling necrosis (p<0.0001) when compared to the non-inoculated control. The observation of new fungi causing Diaporthe seed decay suggests the need for a more comprehensive survey in the U.S. soybean producing areas since members of the genus Diaporthe appear to form a complex that causes seed decay.

Root Rot Caused by Species of Fusarium on Brassica carinata in South Dakota

2018 ◽  
Vol 19 (3) ◽  
pp. 188-192
Author(s):  
Paul N. Okello ◽  
Kristina Petrović ◽  
Brian Kontz ◽  
Shaukat Ali ◽  
Laura F. Marek ◽  
...  
Keyword(s):  
South Dakota ◽  
Root Rot ◽  
Rating Scale ◽  
Fusarium Species ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
The United States ◽  
Brassica Carinata ◽  
Oilseed Crop ◽  
Root Diseases

Brassica carinata is an emerging oilseed crop in the United States, and root diseases caused by Fusarium have the potential to cause yield losses in production. In this study, B. carinata plants were randomly sampled at vegetative and seed development plant stages from South Dakota State University experimental plots. Reddish-brown lesions were observed on roots of sampled plants from which F. acuminatum, F. oxysporum, F. solani, and F. sporotrichioides were recovered. The Fusarium species were identified based on morphology and phylogenetic analyses of the translation elongation factor 1-α gene region. Pathogenicity of the four Fusarium species was evaluated on five B. carinata accessions using a modified inoculum layer method in the greenhouse. At 21 days after inoculation, root rot severity caused by Fusarium on the B. carinata accessions was assessed on a rating scale of 0 to 4 and evaluated using relative treatment effects (RTEs). The F. oxysporum isolate caused significant differences in RTE (P = 0.01) among the B. carinata accessions. However, there were no significant differences in RTE among the B. carinata accessions in response to F. acuminatum (P = 0.82), F. solani (P = 0.76), and F. sporotrichioides (P = 0.47) isolates.

scholarly journals Phylogeny and taxonomic revision of Kernia and Acaulium

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lei Su ◽  
Hua Zhu ◽  
Yongchun Niu ◽  
Yaxi Guo ◽  
Xiaopeng Du ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Large Set ◽  
Internal Transcribed Spacer Region ◽  
Tubulin Genes ◽  
Morphological Criteria ◽  
Molecular Phylogenetic

Abstract The genera Kernia and Acaulium comprise species commonly isolated from dung, soil, decaying meat and skin of animal. The taxonomy of these fungi has been controversial and relies mainly on morphological criteria. With the aim to clarify the taxonomy and phylogeny of these fungi, we studied all the available ex-type strains of a large set of species by means of morphological and molecular phylogenetic analyses. Phylogenetic analysis of the partial internal transcribed spacer region (ITS) and the partial 28S rDNA (LSU) showed that the genera Kernia and Acaulium were found to be separated in two distinct lineages in Microascaceae. Based on morphological characters and multilocus phylogenetic analysis of the ITS, LSU, translation elongation factor 1α and β-tubulin genes, the species in Kernia and Acaulium were well separated and two new combinations are introduced, i.e. Acaulium peruvianum and Acaulium retardatum, a new species of Kernia is described, namely Kernia anthracina. Descriptions of the phenotypic features and molecular phylogeny for identification are discussed for accepted species in two genera in this study.

scholarly journals Cercospora cf. flagellaris and Cercospora cf. sigesbeckiae Are Associated with Cercospora Leaf Blight and Purple Seed Stain on Soybean in North America

2016 ◽  
Vol 106 (11) ◽  
pp. 1376-1385 ◽  
Author(s):  
S. Albu ◽  
R. W. Schneider ◽  
P. P. Price ◽  
V. P. Doyle
Keyword(s):  
United States ◽  
Sexual Reproduction ◽  
Mating Type ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Leaf Blight ◽  
Internal Transcribed Spacer Region ◽  
Type Locus ◽  
Purple Seed Stain

Cercospora kikuchii has long been considered the causal agent of Cercospora leaf blight (CLB) and purple seed stain (PSS) on soybean, but a recent study found C. cf. flagellaris associated with CLB and PSS in Arkansas (United States) and Argentina. Here, we provide a broader perspective on the distribution of C. cf. flagellaris on soybean and alternate hosts within the United States (Arkansas, Louisiana, Mississippi, Missouri, and Kansas). We used a multilocus phylogenetic approach with data from actin, calmodulin, translation elongation factor 1-α, histone 3, the internal transcribed spacer region of rDNA and the mating-type locus to determine that two species, C. cf. flagellaris (200 of 205 isolates) and C. cf. sigesbeckiae (five of 205 isolates), are associated with CLB and PSS in the United States. In our phylogenetic analyses, species-level lineages were generally well-supported, though deeper-level evolutionary relationships remained unresolved, indicating that these genes do not possess sufficient phylogenetic signal to resolve the evolutionary history of Cercospora. We also investigated the potential for sexual reproduction in C. cf. flagellaris in Louisiana by determining the frequency of MAT1-1/MAT1-2 mating-type idiomorphs within the Louisiana population of C. cf. flagellaris. Though the MAT 1-2 idiomorph was significantly more common in our collection, the presence of both mating types suggests the potential for sexual reproduction exists.

scholarly journals Cryptic species of Curvularia in the culture collection of the Queensland Plant Pathology Herbarium

MycoKeys ◽  
2018 ◽  
Vol 35 ◽  
pp. 1-25 ◽  
Author(s):  
Yu Pei Tan ◽  
Pedro W. Crous ◽  
Roger G. Shivas
Keyword(s):  
Plant Pathology ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Culture Collection ◽  
Internal Transcribed Spacer Region ◽  
Translation Elongation ◽  
Air Sample ◽  
Elongation Factor 1

Several unidentified specimens of Curvularia deposited in the Queensland Plant Pathology Herbarium were re-examined. Phylogenetic analyses based on sequence data of the internal transcribed spacer region, partial fragments of the glyceraldehyde-3-phosphate dehydrogenase and the translation elongation factor 1-α genes, supported the introduction of 13 novel Curvularia species. Eight of the species described, namely, C.beasleyi sp. nov., C.beerburrumensis sp. nov., C.eragrosticola sp. nov., C.kenpeggii sp. nov., C.mebaldsii sp. nov., C.petersonii sp. nov., C.platzii sp. nov. and C.warraberensis sp. nov., were isolated from grasses (Poaceae) exotic to Australia. Only two species, C.lamingtonensis sp. nov. and C.sporobolicola sp. nov., were described from native Australian grasses. Two species were described from hosts in other families, namely, C.coatesiae sp. nov. from Litchichinensis (Sapindaceae) and C.colbranii sp. nov. from Crinumzeylanicum (Amaryllidaceae). Curvulariareesii sp. nov. was described from an isolate obtained from an air sample. Furthermore, DNA sequences from ex-type cultures supported the generic placement of C.neoindica and the transfer of Drechsleraboeremae to Curvularia.

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