scholarly journals Molecular Detection of Diverse Leifsonia Strains Associated With Sugarcane

Plant Disease ◽  
2017 ◽  
Vol 101 (8) ◽  
pp. 1422-1431 ◽  
Author(s):  
Anthony J. Young ◽  
Catherine J. Nock
Keyword(s):  
Interspecific Hybrids ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Xylem Sap ◽  
Leaf Sheath ◽  
Ratoon Stunting Disease ◽  
Sugarcane Varieties ◽  
Multiple Samples ◽  
Broad Complex ◽  
Epidemiological Significance

Leifsonia xyli subsp. xyli, causal agent of ratoon stunting disease (RSD) of sugarcane (Saccharum interspecific hybrids), is the most well-known member of the Microbacteriaceae genus Leifsonia. However, the presence of other Leifsonia strains associated with sugarcane has not been reported. A total of 697 Australian and 40 Indonesian sugarcane fields were screened by leaf sheath biopsy (LSB) PCR using primers specific for L. xyli subsp. xyli, in addition to primers designed to amplify DNA from other members of the genus Leifsonia. While L. xyli subsp. xyli was detected in 126 fields, a total of 37 distinct and novel Leifsonia and non-Leifsonia strains were detected in 116 fields. Representatives of these strains were also detected in multiple samples of expressed xylem sap. Sequencing and phylogenetic analyses demonstrated the presence of a broad complex of novel Leifsonia strains, in addition to strains closely related to the recently erected Cnuibacter genus. Attempts to isolate Leifsonia strains were unsuccessful; however, one strain related to Cnuibacter was recovered from expressed xylem sap. Among the genetically diverse lineages discovered, identical genotypes were present in multiple sugarcane varieties growing in disparate regions in different years, strongly suggesting an ongoing association with sugarcane. The epidemiological significance of these strains is unknown, but there is evidence that they can interfere with serological and microscopic RSD diagnostics, and there is the potential that they may represent new and distinct pathologies of sugarcane.

scholarly journals Efficient Diagnosis of Ratoon Stunting Disease of Sugarcane by Quantitative PCR on Pooled Leaf Sheath Biopsies

Plant Disease ◽  
2016 ◽  
Vol 100 (12) ◽  
pp. 2492-2498 ◽  
Author(s):  
Anthony J. Young ◽  
Asuka Kawamata ◽  
Mark A. Ensbey ◽  
Eleanore Lambley ◽  
Catherine J. Nock
Keyword(s):  
Phase Contrast ◽  
Quantitative Polymerase Chain Reaction ◽  
Xylem Sap ◽  
Diagnostic Techniques ◽  
Leaf Sheath ◽  
Conventional Pcr ◽  
Ratoon Stunting Disease ◽  
Contrast Microscopy ◽  
Plate Counts ◽  
Polymerase Chain

Ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli, is arguably one of the most devastating diseases of sugarcane. Four diagnostic techniques were compared for 100 fields of sugarcane (Saccharum interspecific hybrids) of unknown infection status. These were quantitative polymerase chain reaction on pooled leaf sheath biopsies (LSB-qPCR), conventional PCR on the same templates (LSB-PCR), evaporative-binding enzyme immunoassay (EB-EIA) coupled with phase contrast microscopy (PCM) on expressed xylem sap from the same fields, and conventional PCR on the same xylem sap samples. LSB-qPCR and LSB-PCR detected the causal agent in 27 and 18 fields, respectively, whereas, from samples of expressed xylem sap from the same fields, conventional PCR identified 12 infections and EB-EIA/PCM detected L. xyli subsp. xyli in 3 fields. The sensitivities of qPCR and PCR were approximately 103 and 104 CFU ml−1, respectively, determined from plate counts of a dilution series. Tests were conducted on a further 139 LSB samples from across the Australian industry, with qPCR and PCR diagnosing RSD in 31 and 25 fields, respectively. Using qPCR and PCR on LSB samples, RSD was diagnosed in a range of cultivars throughout the year, and qPCR and PCR could detect L. xyli subsp. xyli in sugarcane ranging from 3 months to greater than 1 year old.

scholarly journals Spread and Increase of Ratoon Stunting Disease of Sugarcane and Comparison of Disease Detection Methods

Plant Disease ◽  
1999 ◽  
Vol 83 (12) ◽  
pp. 1170-1175 ◽  
Author(s):  
J. W. Hoy ◽  
M. P. Grisham ◽  
K. E. Damann
Keyword(s):  
Yield Loss ◽  
Detection Method ◽  
Xylem Sap ◽  
Disease Spread ◽  
Detection Methods ◽  
Disease Detection ◽  
Correct Identification ◽  
Dot Blot ◽  
Ratoon Stunting Disease ◽  
Enzyme Immunoassays

The spread and increase of ratoon stunting disease (RSD) resulting from two mechanical harvests were compared in eight sugarcane cultivars at two locations. RSD spread and increase were detected in the ratoon crops grown after each harvest and varied among cultivars and locations. Disease spread and increase were greater in plants grown from stalks collected at the first harvest than in the first ratoon growth from the harvested field. RSD infection was determined using five disease detection methods: alkaline-induced metaxylem autofluorescence; microscopic examination of xylem sap; and dot blot, evaporative-binding, and tissue blot enzyme immunoassays. The tissue blot enzyme immunoassay was the most accurate RSD detection method. The dot blot and evaporative-binding enzyme immunoassays were the least sensitive for detection of RSD-infected stalks, and alkaline-induced metaxylem autofluorescence was least accurate for correct identification of noninfected stalks. The results indicate that disease spread and increase are variable even among cultivars susceptible to yield loss due to RSD, and the greatest threat of disease spread and increase occurs at planting.

scholarly journals Molecular detection of vector borne pathogens in anemic and thrombocytopenic dogs in southern Brazil

2018 ◽  
Vol 27 (4) ◽  
pp. 505-513 ◽  
Author(s):  
Anna Cláudia Baumel Mongruel ◽  
Priscila Ikeda ◽  
Keyla Carstens Marques de Sousa ◽  
Jyan Lucas Benevenute ◽  
Margarete Kimie Falbo ◽  
...  
Keyword(s):  
18S Rrna ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Southern Brazil ◽  
Conventional Pcr ◽  
Pathogenic Potential ◽  
Vector Borne ◽  
Pcr Assays ◽  
Etiological Agents ◽  
Positive Results

Abstract Arthropod-borne pathogens are medically important because of their ability to cause diseases in their hosts. The purpose of this study was to detect the occurrence of Ehrlichia spp., piroplasmids and Hepatozoon spp. in dogs with anemia and thrombocytopenia in southern Brazil. EDTA-whole blood was collected from 75 domestic dogs presenting anemia or/and thrombocytopenia from Guarapuava, state of Paraná, Brazil. DNA samples were subjected to conventional PCR assays for Ehrlichia spp. (dsb), piroplasmids (18S rRNA) and Hepatozoon spp. (18S rRNA), followed by sequencing and phylogenetic analyses. Among the 75 dogs, one (1.33%) was positive for Hepatozoon sp. and six (8%) were positive for piroplasmids in 18S rRNA cPCR assays. None of the dogs showed positive results in Ehrlichia spp.-cPCR targeting dsb gene. The phylogenetic analyses revealed that three piroplasm sequences were clustered with Rangellia vitalii, while one sequence was grouped with B. vogeli. The only sequence obtained from Hepatozoon spp.-PCR protocol was pooled with H. canis. Therefore, there is urgent need for differential molecular diagnosis of the two piroplasm species cited as etiological agents in clinical cases of canine hemoparasitic diseases, given the higher pathogenic potential of R. vitalii than of B. vogeli.

scholarly journals Detection and first molecular characterisation of three picornaviruses from diarrhoeic calves in Turkey

2019 ◽  
Vol 67 (3) ◽  
pp. 463-476
Author(s):  
Hakan Işidan ◽  
Turhan Turan ◽  
Mustafa Ozan Atasoy ◽  
Ibrahim Sözdutmaz ◽  
Bünyamin Irehan
Keyword(s):  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Virus Species ◽  
Specific Primer ◽  
Bovine Enterovirus ◽  
Calf Diarrhoea ◽  
Faecal Samples ◽  
Novel Variants ◽  
Reliable Detection ◽  
Pcr Products

The involvement of picornaviruses in calf diarrhoea was evaluated by the analysis of 127 faecal samples collected from diarrhoeic calves during 2014–2016. Virus detections were carried out by PCR using generic or specific primer pairs. One-third of the faecal samples (33.86%) were found to be positive for one or more of the studied viruses. Bovine kobuvirus was detected in 22.83%, bovine hungarovirus in 11.02%, while bovine enterovirus 1 in 5.51% of the samples. The sequences of the PCR products indicated the existence of novel variants in all the three virus species. When comparing the partial sequences, the nucleotide sequence identities between our newly detected viruses and those previously deposited to the GenBank ranged between 76 and 99%. Phylogenetic analyses revealed a novel lineage within the species Hunnivirus A. Our findings suggest that these viruses should be regarded as possible aetiological agents of calf diarrhoea. Based on the newly determined sequences, we designed and tested a new generic PCR primer set for the more reliable detection of bovine hungaroviruses. This is the first report on the molecular detection of the presence of bovine hungarovirus, bovine kobuvirus and bovine enterovirus 1 in the faecal samples of diarrhoeic calves in Turkey.

scholarly journals Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease

2020 ◽  
Author(s):  
Armelle Marais ◽  
Sergio Murolo ◽  
Chantal Faure ◽  
Yoann Brans ◽  
Clement Larue ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Epidemiological Studies ◽  
Mosaic Disease ◽  
Open Reading Frames ◽  
Sequence Comparisons ◽  
High Incidence ◽  
The Usa ◽  
Reading Frames

Although the chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not elucidated. Here, using classical approaches in combination with high throughput sequencing (HTS) techniques, we identify a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted and sequenced on an Illumina NextSeq500 (2x150 or 2x 75 nt). In each source, we identified a single contig of about 7.2 kilobases that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5% with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons show that this virus is a novel species for which we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak), as well in chestnut trees presenting typical ChMD symptoms in the field (100% and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut SRA transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the USA, as well as ChMV detection in C. dentata from the USA. Preliminary epidemiological studies, performed in France and in Central Eastern Italy, showed that ChMV has a high incidence in some commercial orchards, with a low within-orchard genetic diversity.

Molecular detection and phylogenetic analysis of viruses causing mosaic symptoms in new sugarcane varieties in China

2017 ◽  
Vol 148 (4) ◽  
pp. 931-940 ◽  
Author(s):  
Xiao-Yan Wang ◽  
Wen-Feng Li ◽  
Ying-Kun Huang ◽  
Rong-Yue Zhang ◽  
Hong-Li Shan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Detection ◽  
Sugarcane Varieties

scholarly journals Identification and First Report of Fusarium andiyazi Causing Sheath Rot of Zizania latifolia in China

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1844
Author(s):  
Ya-Min Ma ◽  
Jun-Zi Zhu ◽  
Xiao-Gang Li ◽  
Lai-Liang Wang ◽  
Jie Zhong
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Leaf Sheath ◽  
Pathogenicity Test ◽  
Zizania Latifolia ◽  
First Report ◽  
Perennial Plant ◽  
Fungal Isolates ◽  
Sheath Rot

Zizania latifolia is a perennial plant native to East Asia. The swollen culm of Z. latifolia is a popular vegetable and traditional herbal medicine consumed in China and some other Asian countries. From 2019 to 2021, a sheath rot disease was found in Zhejiang Province of China. Symptoms mainly occurred in the leaf sheath showing as brown necrotic lesions surrounded by yellow halos. The pathogen fungal isolates were isolated from the affected sheaths. Ten representative isolates were selected for morphological and molecular identification by phylogenetic analyses of the translation elongation factor 1-α (TEF1) and the RNA polymerase II subunit beta (RPB2) gene regions. Based on the combined datasets, the fungal isolates were identified as Fusarium andiyazi. Koch’s postulates were confirmed by pathogenicity test, re-isolation and re-identification of the fungal isolates. To the best of our knowledge, this is the first report of sheath rot caused by F. andiyazi in Z. latifolia in China.

scholarly journals Identification of brown rust resistance and molecular detection of <italic>Bru1</italic> gene in new and main cultivated sugarcane varieties

2020 ◽  
Vol 47 (2) ◽  
pp. 376-382
Author(s):  
Rong-Yue ZHANG ◽  
Xiao-Yan WANG ◽  
Kun YANG ◽  
Hong-Li SHAN ◽  
Xiao-Yan CANG ◽  
...  
Keyword(s):  
Rust Resistance ◽  
Molecular Detection ◽  
Brown Rust ◽  
Sugarcane Varieties

scholarly journals The genus Dermoloma is more diverse than expected and forms a monophyletic lineage in the Tricholomataceae

2020 ◽  
Author(s):  
Marisol Sánchez-García ◽  
Katarína Adamčíková ◽  
Pierre-Arthur Moreau ◽  
Alfredo Vizzini ◽  
Soňa Jančovičová ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Taxonomic Diversity ◽  
High Variability ◽  
Species Discrimination ◽  
Continental Scale ◽  
Operational Taxonomic Units ◽  
Monophyletic Lineage ◽  
The Family ◽  
Multiple Samples

Abstract We present the first phylogenetic evaluation of the genus Dermoloma , which is resolved as monophyletic and closely related to Pseudotricholoma , a poorly-known Dermoloma -like lineage within the family Tricholomataceae. The position of Dermoloma is confirmed by the placement of the type species, D. cuneifolium , represented by multiple samples including the neotype. Based on our phylogenetic analyses, we recognised 25 European operational taxonomic units (OTUs), but could only assign species names to ten of them based on ex-type sequences. Furthermore, only five additional published Dermoloma names of uncertain status are available for the remaining 16 potential European species, thus demonstrating an unexpected amount of taxonomic diversity. Samples from Europe and North America seem to be endemic on a continental scale. North American samples formed six unique OTUs, but only one could be reliably named, D. hymenocephalum . Dermoloma is morphologically defined by basidiomata with brown, grey and white colours with a farinaceous odour and a pluristratous hymeniderm type of pileipellis. Our phylogenetic analyses support the subdivision of the genus into two subgenera and four sections, species with inamyloid basidiospores are placed in subg. Dermoloma and those with amyloid basidiospores in subg. Amylospora . Both subgenera are further divided in two sections. The analysis of spore morphology shows that sect. Conica of subg. Dermoloma and sect. Nigrescentia of subg. Amylospora have a very distinctive spore shape. Sect. Atrobrunnea of subg. Amylospora showed relatively high variability of spores among species, but spores of sect. Dermoloma were similar and not useful for species discrimination.

A revision of the New World Euphorbia adiantoides complex (Euphorbiaceae)

Phytotaxa ◽  
2018 ◽  
Vol 350 (3) ◽  
pp. 201
Author(s):  
VICTOR W. STEINMANN ◽  
PABLO CARRILLO-REYES
Keyword(s):  
New World ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Central Mexico ◽  
Northern Population ◽  
Southern Mexico ◽  
Sierra Madre ◽  
Peripatric Speciation ◽  
Nuclear Its ◽  
Multiple Samples

The Euphorbia adiantoides complex is here considered to consist of four species. This group is readily distinguished from other New World Euphorbia by the combination of two unusual features: entire styles with capitate stigmas and dichasial bracts with relatively long, filiform stipules. Euphorbia sonorae is reduced to a synonym of Euphorbia adiantoides, a taxon disjunctly distributed between Mexico and western South America. The other species of the complex are all restricted to Mexico. Two of these are described as new: E. zamudioi, an endemic to the Sierra Madre Oriental, and E. breedlovei, which is widespread in central and southern Mexico. A key to distinguish the species is provided, as too are data concerning their morphology, distribution, habitat, phenology, common names, and uses. Phylogenetic analyses were conducted using the nuclear ITS and the chloroplast psbA-trnH regions and including multiple samples of each species. The phylogenetic results are not always congruent with morphology, and of the four species herein recognized, only Euphorbia zamudioi is suggested to form an exclusive, well-supported lineage. This species is nested within E. breedlovei, and two collections of E. breedlovei from central Mexico are more closely related to E. zamudioi than they are to other E. breedlovei from southern Mexico. We hypothesize that E. zamudioi arose through peripatric speciation, in which a northern population of E. breedlovei became reproductively isolated and morphologically differentiated from the remainder of the populations of E. breedlovei.

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