scholarly journals Development of PCR Assays for the Identification of Species and Pathotypes of Elsinoë Causing Scab on Citrus

Plant Disease ◽  
2007 ◽  
Vol 91 (7) ◽  
pp. 865-870 ◽  
Author(s):  
J. W. Hyun ◽  
N. A. Peres ◽  
S.-Y. Yi ◽  
L. W. Timmer ◽  
K. S. Kim ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sweet Orange ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
The United States ◽  
Specific Primer ◽  
Identification Of Species ◽  
Orange Fruit ◽  
Pcr Assays ◽  
Primer Sets

Two scab pathogens of citrus, Elsinoë fawcettii and E. australis, cause citrus scab and sweet orange scab, respectively, and pathotypes of each species have been described. The two species cannot be readily distinguished by morphological or cultural characteristics and can be distinguished only by host range and the sequence of the internal transcribed spacer (ITS) region. In this study, random amplified polymorphic DNA (RAPD) assays clearly distinguished E. fawcettii and E. australis, and the sweet orange and natsudaidai pathotypes within E. australis also could be differentiated. We developed specific primer sets, Efaw-1 for E. fawcettii; Eaut-1, Eaut-2, Eaut-3, and Eaut-4 for E. australis; and EaNat-1 and EaNat-2 for the natsudaidai pathotype within E. australis using RAPD products unique to each species or pathotype. Other primer sets, Efaw-2 and Eaut-5, which were specific for E. fawcettii and E. australis, respectively, were designed from previously determined ITS sequences. The Efaw-1 and Efaw-2 primer sets successfully identified E. fawcettii isolates from Korea, Australia, and the United States (Florida) and the Eaut-1 to Eaut-5 primer sets identified both the sweet orange pathotype isolates of E. australis from Argentina and the natsudaidai pathotype isolates from Korea. The EaNat-1 and EaNat-2 primer sets were specific for isolates of the natsudaidai pathotype. The Efaw-1 and Efaw-2 primer sets successfully detected E. fawcettii from lesions on diseased leaves and fruit from Korea and primer pairs Eaut-1, Eaut-2, Eaut-3, Eaut-4, and Eaut-5 detected E. australis from lesions on sweet orange fruit from Brazil.

scholarly journals Pathotypes and Genetic Relationship of Worldwide Collections of Elsinoë spp. Causing Scab Diseases of Citrus

2009 ◽  
Vol 99 (6) ◽  
pp. 721-728 ◽  
Author(s):  
J. W. Hyun ◽  
S. H. Yi ◽  
S. J. MacKenzie ◽  
L. W. Timmer ◽  
K. S. Kim ◽  
...  
Keyword(s):  
Host Range ◽  
Sweet Orange ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Elongation Factor ◽  
Its Region ◽  
The United States ◽  
Broad Host Range ◽  
Narrow Host Range ◽  
Rapd Pcr

Two scab diseases are recognized currently on citrus: citrus scab, caused by Elsinoë fawcettii, and sweet orange scab, caused by E. australis. Because the two species cannot be reliably distinguished by morphological or cultural characteristics, host range and molecular methods must be used to identify isolates. Four pathotypes of E. fawcettii and two of E. australis have been described to date based on host range. The host specificity and genetic relationships among 76 isolates from Argentina, Australia, Brazil, Korea, New Zealand, and the United States were investigated. Based on pathogenicity tests on eight differential hosts, 61 isolates were identified as E. fawcettii and 15 as E. australis. Of 61 isolates of E. fawcettii, 24 isolates were identified as the Florida broad host range (FBHR) pathotype, 7 as the Florida narrow host range (FNHR) pathotype, 10 as the Tryon's pathotype, and 3 as the “Lemon” pathotype. Two new pathotypes, the “Jingeul” and the satsuma, rough lemon, grape-fruit, clementine (SRGC), are described, and four isolates did not fit into any of the known pathotypes of E. fawcettii. Of the 15 isolates of E. australis from Argentina and Brazil, 9 belonged to the sweet orange pathotype and 6 from Korea to the natsudaidai pathotype. E. fawcettii and E. australis were clearly distinguishable among groups by random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) assays and the E. fawcettii group was divided into three subgroups, A-1, A-2, and A-3. The A-1 group was composed of the FBHR, FNHR, and SRGC pathotypes; some Lemon pathotypes; and the uncertain isolates. The A-2 subgroup included all of the Tryon's pathotype isolates and one of the three Lemon pathotype isolates and the A-3 group contained the Jingeul pathotype isolates. E. australis was differentiated into two groups: B-1, the natsudaidai pathotype isolates, and B-2, the sweet orange pathotype isolates. Isolates of E. fawcettii and E. australis were clearly distinguishable by sequence analysis of the internal transcribed spacer (ITS) region and the translation elongation factor 1 α (TEF) gene. There were also fixed nucleotide differences in the ITS and TEF genes that distinguished subgroups separated by RAPD-PCR within species. We confirmed two species of Elsinoë, two pathotypes of E. australis, and at least six pathotypes of E. fawcettii and described their distribution in the countries included in this study.

scholarly journals Two new species of Undifilum, fungal endophytes of Astragalus (locoweeds) in the United States

Botany ◽  
2012 ◽  
Vol 90 (9) ◽  
pp. 866-875 ◽  
Author(s):  
Deana L. Baucom ◽  
Marie Romero ◽  
Robert Belfon ◽  
Rebecca Creamer
Keyword(s):  
New Species ◽  
New Mexico ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Fungal Endophytes ◽  
Morphological Characteristics ◽  
Its Region ◽  
The United States ◽  
Neighbor Joining

New species of Undifilum , from locoweeds Astragalus lentiginosus Vitman and Astragalus mollissimus Torr., are described using morphological characteristics and molecular phylogenetic analyses as Undifilum fulvum Baucom & Creamer sp. nov. and Undifilum cinereum Baucom & Creamer sp. nov. Fungi were isolated from dried plants of A. lentiginosus var. araneosus , diphysus , lentiginosus , and wahweapensis collected from Arizona, Oregon, and Utah, USA, and A. mollissimus var. biglovii , earleii , and mollissimus collected from New Mexico, Oklahoma, and Texas, USA. Endophytic fungi from Astragalus locoweeds were compared to Undifilum oxytropis isolates obtained from dried plant material of Oxytropis lamberteii from New Mexico and Oxytropis sericea from Arizona, Colorado, New Mexico, Utah, and Wyoming. Extremely slow growth in vitro was observed for all, and conidia, if present, were ellipsoid with transverse septa. However, in vitro color, growth on four different media, and conidium size differed between fungi from Astragalus spp. and U. oxytropis. Neighbor-joining analyses of internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GPD) gene sequences revealed that U. fulvum and U. cinereum formed a clade distinct from U. oxytropis. This was supported by neighbor-joining analyses of results generated from random amplified polymorphic DNA (RAPD) fragments using two different primers.

scholarly journals Molecular Verification of Bloom-forming Aphanizomenon flos-aquae and Their Secondary Metabolites in the Nakdong River

2018 ◽  
Vol 15 (8) ◽  
pp. 1739 ◽  
Author(s):  
Hae-Kyung Park ◽  
Mi-Ae Kwon ◽  
Hae-Jin Lee ◽  
Jonghee Oh ◽  
Su-Heon Lee ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Water Samples ◽  
Its Region ◽  
Cyanobacterial Blooms ◽  
Specific Primer ◽  
Nakdong River ◽  
Off Flavors ◽  
Primer Sets ◽  
The Nakdong River ◽  
Harmful Cyanobacterial Blooms

Aphanizomenon spp. have formed harmful cyanobacterial blooms in the Nakdong River during spring, autumn, and now in winter, and the expansion of blooming period and area, associated with the global warming is predicted. The genus Aphanizomenon has been described to produce harmful secondary metabolites such as off-flavors and cyanotoxins. Therefore, the production of harmful secondary metabolites from the Aphanizomenon blooms in the Nakdong River needs to be monitored to minimize the risk to both water quality and public health. Here, we sampled the cyanobacterial blooms in the Nakdong River and isolated ten Aphanizomenon strains, morphologically classified as Aphanizomenon flos-aquae Ralfs ex Bornet et Flahault 1888. Phylogenetic analysis using 16S rRNA and internal transcribed spacer (ITS) region nucleotide sequences confirmed this classification. We further verified the harmful secondary metabolites-producing potential of A. flos-aquae isolates and water samples containing cyanobacterial blooms using PCR with specific primer sets for genes involved in biosynthesis of off-flavor metabolites (geosmin) and toxins (microcystins, saxitoxins and cylindrospermopsins). It was confirmed that these metabolite biosynthesis genes were not identified in all isolates and water samples containing only Aphanizomenon spp. Thus, it is likely that there is a low potential for the production of off-flavor metabolites and cyanotoxins in Aphanizomenon blooms in the Nakdong River.

scholarly journals Internal Transcribed Spacer Regions 1 and 2 and Random Amplified Polymorphic DNA Analysis of Didymella bryoniae and Related Phoma Species Isolated from Cucurbits

2002 ◽  
Vol 92 (9) ◽  
pp. 997-1004 ◽  
Author(s):  
Benesh M. Somai ◽  
Ralph A. Dean ◽  
Mark W. Farnham ◽  
Thomas A. Zitter ◽  
Anthony P. Keinath
Keyword(s):  
Disease Severity ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Didymella Bryoniae ◽  
Phylogenetic Groups ◽  
Its Sequence Analysis ◽  
Highly Virulent

Didymella bryoniae (anamorph Phoma cucurbitacearum) is the causal agent of gummy stem blight, although other Phoma species are often isolated from cucurbit plants exhibiting symptoms of the disease. The molecular and phylogenetic relationships between D. bryoniae and these Phoma species are unknown. Isolates of D. bryoniae and Phoma obtained from cucurbits grown at various geographical locations in the United States were subjected to random amplified polymorphic DNA (RAPD) analysis and internal transcribed spacer (ITS) sequence analysis (ITS-1 and ITS-2) to determine the molecular and phylogenetic relationships within and between these fungi. Using RAPD fingerprinting, 59 isolates were placed into four phylogenetic groups, designated RAPD group (RG) I, RG II, RG III, and RG IV. D. bryoniae isolates clustered in either RG I (33 isolates), RG II (12 isolates), or RG IV (one isolate), whereas all 13 Phoma isolates clustered to RG III. There was greater than 99% sequence identity in the ITS-1 and ITS-2 regions between isolates in RG I and RG II, whereas isolates in RG III, P. medicaginis ATCC 64481, and P. exigua ATCC 14728 clustered separately. On muskmelon seedlings, a subset of RG I isolates were highly virulent (mean disease severity was 71%), RG II and RG IV isolates were slightly virulent (mean disease severity was 4%), and RG III isolates were nonpathogenic (disease severity was 0% for all isolates). The ITS sequences indicate that RG I and RG II are both D. bryoniae, but RAPD fingerprints and pathogenicity indicate that they represent two different molecular and virulence subgroups.

scholarly journals Characterization of AG-13, a Newly Reported Anastomosis Group of Rhizoctonia solani

2002 ◽  
Vol 92 (8) ◽  
pp. 893-899 ◽  
Author(s):  
D. E. Carling ◽  
R. E. Baird ◽  
R. D. Gitaitis ◽  
K. A. Brainard ◽  
S. Kuninaga
Keyword(s):  
Rhizoctonia Solani ◽  
Internal Transcribed Spacer ◽  
Aerial Mycelium ◽  
Its Region ◽  
The United States ◽  
Anastomosis Group ◽  
Its Regions ◽  
Cotton Plants ◽  
Agar Surface

Rhizoctonia solani anastomosis group (AG)-13 was collected from diseased roots of field grown cotton plants in Georgia in the United States. Isolates of AG-13 did not anastomose with tester isolates of AG-1 through AG-12. Mycelium of all isolates of AG-13 were light brown but darkened as cultures aged. All isolates produced aerial mycelium. Concentric rings were visible after 3 to 4 days of growth but disappeared as cultures aged and darkened. Individual sclerotia were up to 1.5 mm in diameter, similar in color to the mycelium, and generally embedded in the agar. Clumps of sclerotia up to 5 mm in diameter were produced on the agar surface. All attempts to induce basidiospore production were unsuccessful. The 5.8S region of the rDNA from isolates of AG-13 was identical in length and sequence to isolates of all other AGs of R. solani. Length and sequence of the internal transcribed spacer (ITS) regions of rDNA from isolates of AG-13 were unique among AGs of R. solani. Similarity between AG-13 and other AGs of R. solani ranged from 68 to 85% for ITS region 1 and 85 to 95% for ITS region 2. Selected isolates of AG-13 caused minor or no damage to barley, cauliflower, cotton, lettuce, potato, and radish in laboratory or greenhouse studies.

scholarly journals Characterization of Sphaeropsis sapinea Isolates from South Africa, Mexico, and Indonesia

Plant Disease ◽  
2000 ◽  
Vol 84 (2) ◽  
pp. 151-156 ◽  
Author(s):  
Juanita de Wet ◽  
Michael J. Wingfield ◽  
Teresa A. Coutinho ◽  
Brenda D. Wingfield
Keyword(s):  
United States ◽  
South Africa ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Its Region ◽  
The United States ◽  
Its Sequences ◽  
The Third ◽  
Sphaeropsis Sapinea

Post-hail-associated dieback of Pinus patula and P. radiata trees, induced by Sphaeropsis sapinea (=Diplodia pinea), is a common and important disease in commercial pine plantations. Two morphotypes, A and B, have been described for this fungus based on differences in cultural characteristics, conidial morphology, and virulence among isolates from the north central United States. The existence of the two described morphotypes was later verified through the use of random amplified polymorphic DNA (RAPD) analyses, and the morphotypes were designated as the A and B RAPD marker groups. The objective of this study was to characterize a set of S. sapinea isolates from South Africa, Indonesia, and Mexico using RAPD analysis and DNA sequencing of the internal transcribed spacer (ITS) region of the ribosomal DNA operon. Sizes of conidia and culture morphology were, furthermore, used to compare the three groups of S. sapinea isolates that emerged from the RAPD analysis. Two of the RAPD groups included isolates from the United States, representing the A and B morphotypes, while the third RAPD group accommodated Indonesian and one Mexican isolate. ITS sequences of all the S. sapinea isolates were highly homologous and resolved only the A and B RAPD groups. The ITS sequences of the isolates in the third RAPD group were the same as those of the A RAPD group. Conidia of isolates representing the A and B morphotypes were approximately the same size, but those of the third RAPD group were significantly longer. RAPD analysis enabled us to identify a third group of S. sapinea that is different from the well-recognized A and B groups. Isolates in this third RAPD group also have a distinct morphological characteristic and thus represent a third discrete morphological group, which we refer to as the C morphotype of S. sapinea.

scholarly journals Amplified Fragment Length Polymorphism Analysis and Internal Transcribed Spacer and coxII Sequences Reveal a Species Boundary Within Pythium irregulare

2005 ◽  
Vol 95 (12) ◽  
pp. 1489-1498 ◽  
Author(s):  
Carla D. Garzón ◽  
David M. Geiser ◽  
Gary W. Moorman
Keyword(s):  
Cryptic Species ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Internal Transcribed Spacer ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Its Region ◽  
The United States ◽  
Sensu Stricto ◽  
Pythium Irregulare

Pythium irregulare is a plant-pathogenic oomycete that causes significant damage to a variety of crops, including ornamentals and vegetables. Morphological as well as molecular studies have reported high levels of genetic diversity within P. irregulare sensu lato which has raised the question as to whether it is a single species or is actually a complex of morphologically similar (cryptic) species. In this study, we used amplified fragment length polymorphism (AFLP) fingerprinting and DNA sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal genes (ITS region) and a portion of the mitochondrial cytochrome oxidase II gene and the spacer region between coxI and coxII to characterize 68 isolates of P. irregulare from the United States. The ITS sequence of a P. irregulare neotype at the CBS collection as well as ITS and coxII sequences for P. irregulare, P. spinosum, and P. sylvaticum from previous studies were included in our analysis. Cluster analysis identified a 19-isolate group (IR-II) that separated itself from the rest of the sample (IR-I). Population structure and sequence analyses supported the distinction of IR-I and IR-II and identified IR-II as P. irregulare sensu stricto. IR-I was designated Pythium sp. clade IR-I. Two insertion/deletion mutations and nine nucleotide substitutions in the ITS region and three in the sequence of coxII and the adjacent spacer region separated the two species. Additionally, they differed significantly (P > 0.01) in the frequency of 182 (77%) AFLP alleles. Gene flow results suggested that P. irregulare sensu stricto and Pythium sp. clade IR-I are cryptic species capable of exchanging favorable alleles (Nm = 0.72).

scholarly journals Puccinia hemerocallidis, Cause of Daylily Rust, a Newly Introduced Disease in the Americas

Plant Disease ◽  
2002 ◽  
Vol 86 (11) ◽  
pp. 1194-1198 ◽  
Author(s):  
José R. Hernández ◽  
Mary E. Palm ◽  
Lisa A. Castlebury
Keyword(s):  
United States ◽  
Costa Rica ◽  
Central America ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
The United States

A rust of daylilies was introduced recently into North and Central America. In order to confirm the identity of this rust as Puccinia hemerocallidis, numerous specimens from Costa Rica and the United States were examined morphologically and compared with specimens from China, Japan, Russia, and Taiwan. In addition, the internal transcribed spacer (ITS) region of the ribosomal DNA was sequenced from six representative fresh specimens from the Americas and Asia. We conclude that the rust introduced into the Americas is P. hemerocallidis, for which a modern description is provided with illustrations of the uredinial and telial stages.

scholarly journals Differentiation of a Fusicoccum sp. Causing Panicle and Shoot Blight on California Pistachio Trees from Botryosphaeria dothidea

Plant Disease ◽  
2001 ◽  
Vol 85 (12) ◽  
pp. 1235-1240 ◽  
Author(s):  
Denise R. Smith ◽  
Themis J. Michailides ◽  
Glen R. Stanosz
Keyword(s):  
Internal Transcribed Spacer ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Parsimony Analysis ◽  
Botryosphaeria Dothidea ◽  
Nuclear Rdna ◽  
Shoot Blight ◽  
Blight Disease ◽  
Pistachio Trees

A panicle and shoot blight disease of pistachio trees in California is caused by a fungus previously identified as the anamorph of Botryosphaeria dothidea. We have compared random amplified polymorphic DNA (RAPD) markers, nuclear rDNA internal transcribed spacer (ITS) region sequences, and conidium morphology of 15 isolates of the pistachio Fusicoccum to those of well-characterized isolates of B. dothidea, B. ribis, and F. luteum. Cluster analysis of RAPD markers separated the pistachio Fusicoccum isolates from B. dothidea, as did parsimony analysis of the ITS region sequences. Conidium size and shape were similar to those of B. ribis (Fusicoccum sp.) and F. luteum, but distinguishable from those of F. aesculi (the anamorph of B. dothidea). We conclude that the fungus causing panicle and shoot blight of pistachio is distinguishable from B. dothidea and is part of a complex containing B. ribis, F. luteum, and other fungi with Fusicoccum anamorphs.

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