scholarly journals Armillaria Root-Rot Pathogens: Species Boundaries and Global Distribution

Pathogens ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 83 ◽  
Author(s):  
Martin Coetzee ◽  
Brenda Wingfield ◽  
Michael Wingfield
Keyword(s):  
Dna Sequence ◽  
Root Rot ◽  
Sequence Data ◽  
Current Knowledge ◽  
Single Gene ◽  
Intergenic Spacer ◽  
Species Boundaries ◽  
Intergenic Spacer Region ◽  
Biogeographic History ◽  
Armillaria Root Rot

This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.

scholarly journals First Report of Armillaria gallica Causing Armillaria Root Rot in Daylily in South Carolina

Plant Disease ◽  
2005 ◽  
Vol 89 (6) ◽  
pp. 683-683 ◽  
Author(s):  
G. Schnabel ◽  
K. E. Bussey ◽  
P. K. Bryson
Keyword(s):  
South Carolina ◽  
Root Rot ◽  
Intergenic Spacer ◽  
Selective Medium ◽  
Sodium Hypochlorite Solution ◽  
First Report ◽  
Intergenic Spacer Region ◽  
Hardwood Trees ◽  
Armillaria Root Rot ◽  
Armillaria Gallica

Daylily (Hemerocallis sp.) plants declined in a homeowner's backyard in Walhalla, SC in June 2004. The backyard in northwestern South Carolina contained multiple, hardwood tree stumps, was surrounded by mature hardwood trees, and contained a dogwood tree showing symptoms of Armillaria root rot. Daylily plants were stunted and necrosis of leaves began at the leaf tips. A cross section through the crown of the wilting plants revealed necrotic areas with the presence of white mycelial fans. Rhizomorphs were found in the direct vicinity of the daylily root system, on the roots of the dogwood, and throughout surrounding soil. Diseased daylily crowns, rhizomorphs, and dogwood bark containing mycelial fans were collected. Small sections of white mycelial fans from daylily crowns and the dogwood sample were transferred to benomyl dichloran streptomycin (BDS) selective medium. Rhizomorph pieces were surface sterilized in a 0.6% sodium hypochlorite solution for 10 min and rinsed with sterile water before being transferred to BDS selective medium. Fungal cultures from all three sources looked similar on BDS medium and developed mainly crustose mycelium with some parts being aerial. After 1 week of incubation at room temperature in the dark, all cultures developed nonmelanized, mycelial fans that initiated from the center of the colony. The nucleotide sequences of internal transcribed spacer regions 1 and 2 and the intergenic spacer region 1 were identical for all isolates, and a BLAST search in GenBank of these sequences confirmed the identity of the pathogen as A. gallica (Marxmueller & Romagnesi) for both loci. To our knowledge, this is the first report of A. gallica causing disease on Hemerocallis spp. Our findings indicate that daylilies might be at risk for infection and should not be cultivated in soils containing rhizomorphs from pathogenic Armillaria species.

scholarly journals Mismatch induced speciation in Salmonella : model and data

2006 ◽  
Vol 361 (1475) ◽  
pp. 2045-2053 ◽  
Author(s):  
Daniel Falush ◽  
Mia Torpdahl ◽  
Xavier Didelot ◽  
Donald F Conrad ◽  
Daniel J Wilson ◽  
...  
Keyword(s):  
New Species ◽  
Natural Selection ◽  
Dna Sequence ◽  
Computer Simulations ◽  
De Novo ◽  
Sequence Data ◽  
Biological Species ◽  
Species Boundaries ◽  
Population Subdivision ◽  
Geographical Population

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella , without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

Species boundaries within Saprolegnia (Saprolegniales, Oomycota) based on morphological and DNA sequence data

Mycologia ◽  
2007 ◽  
Vol 99 (3) ◽  
pp. 421-429 ◽  
Author(s):  
J. P. Hulvey ◽  
D. E. Padgett ◽  
J. C. Bailey
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Species Boundaries ◽  
Dna Sequence Data

scholarly journals Molecular Detection and Characterization of Borrelia garinii (Spirochaetales: Borreliaceae) in Ixodes nipponensis (Ixodida: Ixodidae) Parasitizing a Dog in Korea

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 289 ◽  
Author(s):  
Seung-Hun Lee ◽  
Youn-Kyoung Goo ◽  
Paul John L. Geraldino ◽  
Oh-Deog Kwon ◽  
Dongmi Kwak
Keyword(s):  
Molecular Detection ◽  
Single Gene ◽  
Protein A ◽  
Intergenic Spacer ◽  
Surface Protein ◽  
23S Rrna ◽  
Borrelia Garinii ◽  
Intergenic Spacer Region ◽  
Individual Level ◽  
Pcr Targeting

The present study aimed to detect and characterize Borrelia spp. in ticks attached to dogs in Korea. Overall, 562 ticks (276 pools) attached to dogs were collected and tested for Borrelia infection by PCR targeting the 5S-23S rRNA intergenic spacer region (rrf-rrl). One tick larva (pool level, 0.4%; individual level, 0.2%) was confirmed by sequencing Borrelia garinii, a zoonotic pathogen. For molecular characterization, the outer surface protein A (ospA) and flagellin genes were analyzed. Phylogenetic ospA analysis distinguished B. garinii from B. bavariensis, which has been recently identified as a novel Borrelia species. On the other hand, phylogenetic analysis showed that single gene analysis involving rrf-rrl or flagellin was not sufficient to differentiate B. garinii from B. bavariensis. In addition, the B. garinii-infected tick was identified as Ixodes nipponensis by sequencing according to mitochondrial 16S rRNA and the second transcribed spacer region. To our knowledge, this is the first study to report the molecular detection of B. garinii in I. nipponensis parasitizing a dog in Korea. Continuous monitoring of tick-borne pathogens in ticks attached to animals is required to avoid disease distribution and possible transmission to humans.

scholarly journals Differentiation of Moraxella Bovoculi sp. nov. from other Coccoid Moraxellae by the Use of Polymerase Chain Reaction and Restriction Endonuclease Analysis of Amplified DNA

2007 ◽  
Vol 19 (5) ◽  
pp. 532-534 ◽  
Author(s):  
John A. Angelos ◽  
Louise M. Ball
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Restriction Analysis ◽  
Intergenic Spacer ◽  
Restriction Enzyme Digestion ◽  
Chain Reaction ◽  
Gram Negative ◽  
Intergenic Spacer Region ◽  
Polymerase Chain ◽  
Moraxella Bovoculi

Moraxella oris was historically the only coccoid Moraxella identified in cultures of ocular fluid from cattle with infectious bovine keratoconjunctivitis (IBK) and could be morphologically and biochemically differentiated from Moraxella bovis. Moraxella bovoculi sp. nov. is a recently characterized Moraxella isolated from ulcerated eyes of calves with IBK in northern California in 2002. Like Moraxella ovis, M. bovoculi sp. nov. is a gram-negative coccus/diplococcus. All 18 original isolates of M. bovoculi sp. nov. possessed phenylalanine deaminase (PADase) activity and could therefore be differentiated from M. ovis and M. bovis. During the characterization of 44 additional isolates of hemolytic gram-negative cocci that were cultured from ulcerated eyes of IBK-affected calves, 2 PADase-negative isolates were identified that could not be differentiated biochemically from M. ovis; however, the DNA sequence of the 16S-23S intergenic spacer region (ISR) of the isolates matched the 16S-23S ISR DNA sequence of M. bovoculi sp. nov. To facilitate the identification of PADase-negative moraxellae, a polymerase chain reaction (PCR) coupled with restriction enzyme digestion analysis of amplified DNA was developed. Amplification of the 16S-23S ISR followed by AfaI digestion of amplified DNA could differentiate M. bovoculi sp. nov. from M. ovis and other moraxellae. The DNA sequence analysis of the amplified 16S-23S ISR from the 42 PADase-positive isolates of hemolytic gram-negative cocci indicated that all were M. bovoculi sp. nov. and all possessed an AfaI site. A PCR coupled with restriction analysis of amplified DNA can aid in identifying M. bovoculi sp. nov.

scholarly journals The intergenic spacer region of the ribosomal RNA gene of Penicillium marneffei shows almost no DNA sequence diversity

2010 ◽  
Vol 54 (11) ◽  
pp. 714-716 ◽  
Author(s):  
Nanthawan Mekha ◽  
Takashi Sugita ◽  
Koichi Makimura ◽  
Natteewan Poonwan ◽  
Pathom Sawanpanyalert ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Ribosomal Rna ◽  
Intergenic Spacer ◽  
Sequence Diversity ◽  
Penicillium Marneffei ◽  
Ribosomal Rna Gene ◽  
Intergenic Spacer Region

Delimiting species boundaries for endangered Canary Island grasshoppers based on DNA sequence data

2006 ◽  
Vol 8 (3) ◽  
pp. 587-598 ◽  
Author(s):  
Heriberto López ◽  
Hermans G. Contreras-Díaz ◽  
Pedro Oromí ◽  
Carlos Juan
Keyword(s):  
Dna Sequence ◽  
Canary Island ◽  
Sequence Data ◽  
Species Boundaries ◽  
Dna Sequence Data
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