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

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.

Download Full-text

Pathological Characterization and Molecular Analysis of Elsinoe Isolates Causing Scab Diseases of Citrus in Jeju Island in Korea

Plant Disease ◽

10.1094/pdis.2001.85.9.1013 ◽

2001 ◽

Vol 85 (9) ◽

pp. 1013-1017 ◽

Cited By ~ 29

Author(s):

J.-W. Hyun ◽

L. W. Timmer ◽

S.-C. Lee ◽

S.-H. Yun ◽

S.-W. Ko ◽

...

Keyword(s):

Host Range ◽

Sweet Orange ◽

Random Amplified Polymorphic Dna ◽

Jeju Island ◽

Broad Host Range ◽

Narrow Host Range ◽

Satsuma Mandarin ◽

Rough Lemon ◽

Differential Hosts ◽

Cleopatra Mandarin

Two scab diseases are recognized currently on citrus: (i) citrus scab caused by Elsinoe fawcettii, which has several pathotypes; and (ii) sweet orange scab caused by E. australis. Pathogenicity and cultural characteristics among 36 isolates collected from Jeju Island were investigated. Of 30 isolates from satsuma mandarin, yuzu, and kinkoji, all were E. fawcettii; 27 were similar to the Florida broad host range pathotype and 3 were similar to the Florida narrow host range pathotype by inoculation of differential hosts. Six isolates from natsudaidai were nonpathogenic to satsuma mandarin, rough lemon, sour orange, grapefruit, cleopatra mandarin, and natsudaidai leaves, and were only pathogenic to natsudaidai fruit. Isolates from natsudaidai usually produced unique tomentose colonies on potato dextrose agar compared with isolates from other citrus species. The colonies were relatively fast growing, radially sulcate, larger, and more expansive than the gummy, mucoid colonies of other isolates. Isolates from Florida, Australia, Argentina, and Jeju Island (Korea) were genetically differentiated using random amplified polymorphic DNA markers. E. fawcettii from Korea, Florida, and Australia, E. australis from Argentina, and natsudaidai isolates clustered closely within groups, but were clearly distinguishable among groups.

Download Full-text

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

Plant Disease ◽

10.1094/pdis-91-7-0865 ◽

2007 ◽

Vol 91 (7) ◽

pp. 865-870 ◽

Cited By ~ 16

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.

Download Full-text

Host specificity and vegetative compatibility of Dutch isolates of Fusarium oxysporum f.sp. asparagi

Canadian Journal of Botany ◽

10.1139/b97-041 ◽

1997 ◽

Vol 75 (3) ◽

pp. 383-393 ◽

Cited By ~ 21

Author(s):

Wim J. Blok ◽

Gerrit J. Bollen

Keyword(s):

Fusarium Oxysporum ◽

Host Range ◽

Plant Species ◽

Root Rot ◽

The United States ◽

Vegetative Compatibility ◽

Broad Host Range ◽

Vegetative Compatibility Groups ◽

Narrow Host Range

The host range of Fusarium oxysporum f.sp. asparagi (Foa) was studied in inoculation experiments with 21 plant species. Typical root rot symptoms were incited only in asparagus, in all experiments; lupin and pea were susceptible under in vitro conditions but showed only mild symptoms occasionally when tested in soil; none of the other species showed external disease symptoms. Root colonization by Foa was studied for 14 plant species. The pathogen was detected in externally disinfested roots of all species except leek and onion, with asparagus the most extensively colonized species. Asparagus was not susceptible to isolates of F. oxysporum f.sp. pisi, lupini, cepae, lilii, and gladioli and Fusarium sacchari var. elongatum. Naturally infested field soil was planted twice for 11 – 13 weeks with 11 plant species, including asparagus and several symptomless hosts, and subsequently with asparagus as a biotest plant. Of these crops, only asparagus greatly increased the severity of Foa root rot. It was concluded that Foa has a narrow host range as a pathogen but a broad host range as a parasite. The consequences of the latter for the epidemiology of Foa are discussed. Twenty-four Foa isolates were assigned to 18 different vegetative compatibility groups (VCGs); three additional F. oxysporum isolates, which were not pathogenic on asparagus, each belonged to a unique VCG. These findings indicate that the Dutch Foa population is very diverse genetically, as was found previously for the Foa population in the United States. Key words: asparagus, Fusarium oxysporum f.sp. asparagi, host range, lupin, pea, symptomless hosts, vegetative compatibility.

Download Full-text

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

Botany ◽

10.1139/b2012-056 ◽

2012 ◽

Vol 90 (9) ◽

pp. 866-875 ◽

Cited By ~ 33

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.

Download Full-text

Evolution of IncA/CblaCMY-2-Carrying Plasmids by Acquisition of theblaNDM-1Carbapenemase Gene

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05116-11 ◽

2011 ◽

Vol 56 (2) ◽

pp. 783-786 ◽

Cited By ~ 83

Author(s):

Alessandra Carattoli ◽

Laura Villa ◽

Laurent Poirel ◽

Rémy A. Bonnin ◽

Patrice Nordmann

Keyword(s):

Host Range ◽

Large Scale ◽

The United States ◽

Broad Host Range ◽

New Delhi ◽

Yersinia Ruckeri ◽

Content Type ◽

Photobacterium Damselae ◽

Environmental Bacteria ◽

Broad Host Range Plasmids

ABSTRACTTheblaNDM-1gene has been reported to be often located on broad-host-range plasmids of the IncA/C type in clinical but also environmental bacteria recovered from the New Delhi, India, area. IncA/C-type plasmids are the main vehicles for the spread of the cephalosporinase geneblaCMY-2, frequently identified in the United States, Canada, and Europe. In this study, we completed the sequence of IncA/C plasmid pNDM-KN carrying theblaNDM-1gene, recovered from aKlebsiella pneumoniaeisolate from Kenya. This sequence was compared with those of three IncA/C-type reference plasmids fromEscherichia coli,Yersinia ruckeri, andPhotobacterium damselae. Comparative analysis showed that theblaNDM-1gene was located on a widely diffused plasmid scaffold known to be responsible for the spread ofblaCMY-2-like genes and consequently for resistance to broad-spectrum cephalosporins. Considering that IncA/C plasmids possess a broad host range, this scaffold might support a large-scale diffusion of theblaNDM-1gene among Gram-negative rods.

Download Full-text

Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola

Plant Disease ◽

10.1094/pdis-10-18-1819-re ◽

2019 ◽

Vol 103 (11) ◽

pp. 2893-2902 ◽

Cited By ~ 3

Author(s):

Shaista Karim ◽

R. Ryan McNally ◽

Afnan S. Nasaruddin ◽

Alexis DeReeper ◽

Ramil P. Mauleon ◽

...

Keyword(s):

Host Range ◽

Bacterial Pathogen ◽

The United States ◽

Broad Host Range ◽

Software Pipeline ◽

Widespread Occurrence ◽

Field Samples ◽

Primer Sets ◽

Genome Analyses ◽

User Friendly

Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.

Download Full-text

Emergence and Dissemination of Enterobacteriaceae Isolates Producing CTX-M-1-Like Enzymes in Spain Are Associated with IncFII (CTX-M-15) and Broad-Host-Range (CTX-M-1, -3, and -32) Plasmids

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01070-06 ◽

2006 ◽

Vol 51 (2) ◽

pp. 796-799 ◽

Cited By ~ 82

Author(s):

Ângela Novais ◽

Rafael Cantón ◽

Raquel Moreira ◽

Luísa Peixe ◽

Fernando Baquero ◽

...

Keyword(s):

Host Range ◽

Broad Host Range ◽

Narrow Host Range

ABSTRACT The spread of CTX-M-1-like enzymes in Spain is associated with particular plasmids of broad-host-range IncN (bla CTX-M-32, bla CTX-M-1), IncL/M (bla CTX-M-1), and IncA/C2 (bla CTX-M-3) or narrow-host-range IncFII (bla CTX-M-15). The identical genetic surroundings of bla CTX-M-32 and bla CTX-M-1 and their locations on related 40-kb IncN plasmids indicate the in vivo evolution of this element.

Download Full-text

A revision of species of the genus Haematoloechus Looss, 1899 (Trematoda: Haematoloechidae) from Canada and the United States

Canadian Journal of Zoology ◽

10.1139/z81-252 ◽

1981 ◽

Vol 59 (9) ◽

pp. 1836-1846 ◽

Cited By ~ 16

Author(s):

Murray J. Kennedy

Keyword(s):

United States ◽

Host Range ◽

Geographical Variation ◽

Rana Catesbeiana ◽

Field Studies ◽

The United States ◽

Valid Species ◽

Narrow Host Range ◽

Species Groups ◽

Degree Of Maturity

Previous experimental and field studies have shown that variations within the genus Haematoloechus may result from differences in age and degree of maturity, extent of crowding, species of host, and other factors.Based on these observations, only 6 of the 15 previously known species from Canada and the United States are considered valid. The valid species and their synonyms are as follows: Haematoloechus longiplexus Stafford, 1902; H. breviplexus Stafford, 1902; H. varioplexus Stafford, 1902 (= H. parviplexus, = H. buttensis, = H. similiplexus, = H. floedae, and H. uniplexus); H. kernensis Ingles, 1932 (= H. tumidus); H. medioplexus Stafford, 1902; and H. complexus (Seely, 1906) (= H. coloradensis, = H. confusus, = H. oxyorchis).The existence of three species groups is hypothesized. Haematoloechus longiplexus and H. breviplexus constitute one group, characterized by little geographical variation and a narrow host range. They are typically parasites of Rana catesbeiana and R. clamitans. Haematoloechus varioplexus and H. kernensis constitute the second group. These species have a wider host range and greater variation in characters purported to be specific differences. The third group includes those lung flukes which do not contain extracaecal loops (H. medioplexus and H. complexus). Of these, only H. medioplexus had little geographical variation and was found to occur in a single frog host.

Download Full-text

Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

BMC Genomics ◽

10.1186/s12864-021-07637-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Rachel Rattner ◽

Shree Prasad Thapa ◽

Tyler Dang ◽

Fatima Osman ◽

Vijayanandraj Selvaraj ◽

...

Keyword(s):

Genetic Diversity ◽

Host Range ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

The United States ◽

Weed Species ◽

Protein Coding ◽

Spiroplasma Citri ◽

Beet Leafhopper ◽

Separate Branch

Abstract Background Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen’s wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas. Results Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3–3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3–3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. Conclusions The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1597–2232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3–3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.

Download Full-text

Genetic Relatedness among Environmental, Clinical, and Diseased-Eel Vibrio vulnificus Isolates from Different Geographic Regions by Ribotyping and Randomly Amplified Polymorphic DNA PCR

Applied and Environmental Microbiology ◽

10.1128/aem.64.9.3403-3410.1998 ◽

1998 ◽

Vol 64 (9) ◽

pp. 3403-3410 ◽

Cited By ~ 37

Author(s):

Covadonga R. Arias ◽

María Jesús Pujalte ◽

Esperanza Garay ◽

Rosa Aznar

Keyword(s):

Genetic Relatedness ◽

Vibrio Vulnificus ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Mediterranean Coast ◽

Universal Primers ◽

23S Rrna ◽

Rrna Gene ◽

Conserved Sequence ◽

Rapd Pcr

ABSTRACT Genetic relationships among 132 strains of Vibrio vulnificus (clinical, environmental, and diseased-eel isolates from different geographic origins, as well as seawater and shellfish isolates from the western Mediterranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with KpnI and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Random amplification of DNA was performed with M13 and T3 universal primers. The comparison between ribotyping and RAPD PCR revealed an overall agreement regarding the high level of homogeneity of diseased-eel isolates in contrast to the genetic heterogeneity of Mediterranean isolates. The latter suggests the existence of autochthonous clones present in Mediterranean coastal waters. Both techniques have revealed a genetic proximity among Spanish fish farm isolates and a close relationship between four Spanish eel farm isolates and some Mediterranean isolates. Whereas the differentiation within diseased-eel isolates was only possible by ribotyping, RAPD PCR was able to differentiate phenotypically atypical isolates of V. vulnificus. On the basis of our results, RAPD PCR is proposed as a better technique than ribotyping for rapid typing in the routine analysis of new V. vulnificusisolates.

Download Full-text