scholarly journals Multilocus Genotyping Reveals New Molecular Markers for Differentiating Distinct Genetic Lineages among “Candidatus Phytoplasma Solani” Strains Associated with Grapevine Bois Noir

Pathogens ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 970
Author(s):  
Alessandro Passera ◽  
Yan Zhao ◽  
Sergio Murolo ◽  
Roberto Pierro ◽  
Emilija Arsov ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Type A ◽  
Sequence Variants ◽  
Typing Method ◽  
Translation Elongation ◽  
Bois Noir ◽  
Genetic Lineages ◽  
Ecological Complexity ◽  
Genes Encoding

Grapevine Bois noir (BN) is associated with infection by “Candidatus Phytoplasma solani” (CaPsol). In this study, an array of CaPsol strains was identified from 142 symptomatic grapevines in vineyards of northern, central, and southern Italy and North Macedonia. Molecular typing of the CaPsol strains was carried out by analysis of genes encoding 16S rRNA and translation elongation factor EF-Tu, as well as eight other previously uncharacterized genomic fragments. Strains of tuf-type a and b were found to be differentially distributed in the examined geographic regions in correlation with the prevalence of nettle and bindweed. Two sequence variants were identified in each of the four genomic segments harboring hlyC, cbiQ-glyA, trxA-truB-rsuA, and rplS-tyrS-csdB, respectively. Fifteen CaPsol lineages were identified based on distinct combinations of sequence variations within these genetic loci. Each CaPsol lineage exhibited a unique collective restriction fragment length polymorphism (RFLP) pattern and differed from each other in geographic distribution, probably in relation to the diverse ecological complexity of vineyards and their surroundings. This RFLP-based typing method could be a useful tool for investigating the ecology of CaPsol and the epidemiology of its associated diseases. Phylogenetic analyses highlighted that the sequence variants of the gene hlyC, which encodes a hemolysin III-like protein, separated into two clusters consistent with the separation of two distinct lineages on the basis of tufB gene sequences. Alignments of deduced full protein sequences of elongation factor-Tu (tufB gene) and hemolysin III-like protein (hlyC gene) revealed the presence of critical amino acid substitutions distinguishing CaPsol strains of tuf-type a and b. Findings from the present study provide new insights into the genetic diversity and ecology of CaPsol populations in vineyards.

Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus

2012 ◽  
Vol 25 (6) ◽  
pp. 418 ◽  
Author(s):  
Roy E. Halling ◽  
Mitchell Nuhn ◽  
Todd Osmundson ◽  
Nigel Fechner ◽  
James M. Trappe ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sister Group ◽  
Molecular Data ◽  
Translation Elongation ◽  
Spore Deposit ◽  
Large Subunit Rdna ◽  
Translation Elongation Factor 1Α

Harrya is described as a new genus of Boletaceae to accommodate Boletus chromapes, a pink-capped bolete with a finely scabrous stipe adorned with pink scabers, a chrome yellow base and a reddish-brown spore deposit. Phylogenetic analyses of large-subunit rDNA and translation elongation factor 1α confirmed Harrya as a unique generic lineage with two species, one of which is newly described (H. atriceps). Some Chinese taxa were recently placed in a separate genus, Zangia, supported by both morphology and molecular data. Multiple accessions from Queensland, Australia, support the synonymy of at least three species in a separate Australian clade in the new genus, Australopilus. The truffle-like Royoungia is also supported as a separate lineage in this clade of boletes. Even though it lacks stipe characters, it possesses the deep, bright yellow to orange pigments in the peridium. Additional collections from Zambia and Thailand represent independent lineages of uncertain phylogenetic placement in the Chromapes complex, but sampling is insufficient for formal description of new species. Specimens from Java referable to Tylopilus pernanus appear to be a sister group of the Harrya lineage.

Baorangia duplicatopora (Boletaceae, Boletales), a new bolete from tropical China

Phytotaxa ◽  
2021 ◽  
Vol 508 (1) ◽  
Author(s):  
XU ZHANG ◽  
ZHI-QUN LIANG ◽  
SHUAI JIANG ◽  
CHANG XU ◽  
XIN-HUA FU ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Its Region ◽  
Tropical Region ◽  
Translation Elongation ◽  
Line Drawings ◽  
Microscopic Features ◽  
Tropical China

Baorangia duplicatopora is described as a new species from Hainan Province, a tropical region of China. It is morphologically characterized by large to very large basidiomata with a dull rose red, rose pink to purplish red pileus, compound pores, pileus context near hymenophore and stipe context staining blue when injured, a red stipe, and cheilocystidia wider than those of other Baorangia species. Phylogenetic analyses of DNA sequences from part of the 28S gene, the nuc rDNA internal transcribed spacer (ITS) region, and part of the translation elongation factor 1-α gene (TEF1) also confirmed that B. duplicatopora forms an independent lineage within Baorangia. Detailed descriptions, color photographs of fresh basidiomata, and line drawings of microscopic features of the new species are presented. A key to species of Baorangia in the world is also provided.

Spegazzinia camelliae sp. nov. (Didymosphaeriaceae, Pleosprales), a new endophytic fungus from northern Thailand

Phytotaxa ◽  
2021 ◽  
Vol 483 (2) ◽  
pp. 117-128
Author(s):  
NAKARIN SUWANNARACH ◽  
JATURONG KUMLA ◽  
SAISAMORN LUMYONG
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Full Description ◽  
Translation Elongation ◽  
Spine Length ◽  
Elongation Factor 1 Alpha

A new endophytic ascomycete, described herein as Spegazzinia camelliae, was isolated from leaves of Camellia sinensis var. assamica collected from Nan Province, Thailand. This species is characterized by basauxic conidiophores and dark brown to blackish brown α and β conidia. It can be distinguished from previously described Spegazzinia species by the spine length of the α conidia and the size of the β conidia. Multi-gene phylogenetic analyses of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) of the nuclear ribosomal DNA (rDNA) and the translation elongation factor 1-alpha (tef1) genes also support S. camelliae is a distinct new species within Spegazzinia. A full description, color photographs, illustrations and a phylogenetic tree showing the position of S. camelliae are provided.

A new species of Heimioporus (Boletaceae) from southern China

Phytotaxa ◽  
2019 ◽  
Vol 415 (4) ◽  
pp. 179-188
Author(s):  
XIANG-NYU CHEN ◽  
MING ZHANG ◽  
TAI-HUI LI ◽  
NIAN-KAI ZENG
Keyword(s):  
New Species ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Morphological Characters ◽  
Molecular Data ◽  
Translation Elongation ◽  
Distinct Member ◽  
Elongation Factor 1 ◽  
A New Species

Heimioporus sinensis, collected from tropical and subtropical areas of China, is introduced as a new species based on both morphological characters and molecular data. The species is characterized by the purplish red to deep magenta pileus, the reticulated stipe, the irregularly reticulate to reticulate-alveolate basidiospores 11.5–13.5 × 8–9.5 μm, and a trichodermal to intricately trichodermal pileipellis. Phylogenetic analyses based on the nuc 28S rDNA D1-D2 domains (28S) and the translation elongation factor 1-α gene (tef1-α) showed that H. sinensis is a distinct member of the genus Heimioporus in the subfamily Xerocomoideae.

scholarly journals Multi-gene phylogeny and taxonomy of Amauroderma s. lat. (Ganodermataceae)

2020 ◽  
Vol 44 (1) ◽  
pp. 206-239 ◽  
Author(s):  
Y.-F. Sun ◽  
D.H. Costa-Rezende ◽  
J.-H. Xing ◽  
J.-L. Zhou ◽  
B. Zhang ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Examination ◽  
Translation Elongation ◽  
Multiple Loci ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

Amauroderma s.lat. has been defined mainly by the morphological features of non-truncate and double-walled basidiospores with a distinctly ornamented endospore wall. In this work, taxonomic and phylogenetic studies on species of Amauroderma s.lat. are carried out by morphological examination together with ultrastructural observations, and molecular phylogenetic analyses of multiple loci including the internal transcribed spacer regions (ITS), the large subunit of nuclear ribosomal RNA gene (nLSU), the largest subunit of RNA polymerase II (RPB1) and the second largest subunit of RNA polymerase II (RPB2), the translation elongation factor 1-α gene (TEF) and the β-tubulin gene (TUB). The results demonstrate that species of Ganodermataceae formed ten clades. Species previously placed in Amauroderma s.lat. are divided into four clades: Amauroderma s.str., Foraminispora, Furtadoa and a new genus Sanguinoderma. The classification of Amauroderma s. lat. is thus revised, six new species are described and illustrated, and eight new combinations are proposed. SEM micrographs of basidiospores of Foraminispora and Sanguinoderma are provided, and the importance of SEM in delimitation of taxa in this study is briefly discussed. Keys to species of Amauroderma s.str., Foraminispora, Furtadoa, and Sanguinoderma are also provided.

Diaporthe sinensis, a new fungus from Amaranthus sp. in China 

Phytotaxa ◽  
2019 ◽  
Vol 425 (5) ◽  
pp. 259-268
Author(s):  
XIAO-XIAO FENG ◽  
JIA-JIE CHEN ◽  
GUO-RONG WANG ◽  
TING-TING CAO ◽  
YONG-LI ZHENG ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Fungal Species ◽  
Translation Elongation Factor ◽  
Translation Elongation ◽  
Stems And Leaves ◽  
Elongation Factor 1 ◽  
Β Tubulin

During an exploration of plant pathogens in vegetables occuring in Zhejiang province, China, a novel fungal species, was found. Three strains ZJUP0033-4, ZJUP0038-3 and ZJUP0132 were isolated from black round lesions in the stems and leaves of Amaranthus sp. Phylogenetic analyses based on sequences from four genes including rDNA internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α), histone (HIS) and β-tubulin (TUB) indicated that D. sinensis clustered in a distinct clade closely related to D. neoarctii, D. angelicae, D. subordinaria, D. arctii, D. cuppatea, D. lusitanicae, D. novem, D. infecunda, D. ganjae and D. manihotia. Morphologically, D. sinensis is distinguished by brown, scattered, globose pycnidia and ellipsoid alpha conidia with bi- to multiguttulate.

Saprobic Dothideomycetes in Thailand: Phaeoseptum hydei sp. nov., a new terrestrial ascomycete in Phaeoseptaceae

Phytotaxa ◽  
2020 ◽  
Vol 449 (2) ◽  
pp. 149-163
Author(s):  
DHANUSHKA N. WANASINGHE ◽  
PETER E. MORTIMER ◽  
CHANOKNED SENWANNA ◽  
RATCHADAWAN CHEEWANGKOON
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
University Campus ◽  
Translation Elongation ◽  
Delonix Regia ◽  
The Family ◽  
Elongation Factor 1 Alpha ◽  
Vertical Septum ◽  
Elongation Factor 1

During a survey of saprobic microfungi in Thailand, a dothideomycetous fungus was found on a dead twig of Delonix regia, on the Chiang Mai University campus. This fungus is characterized by fully immersed ascomata under a small blackened pseudoclypeus, pseudoparenchymatous peridium, cellular pseudoparaphyses, cylindrical-clavate asci with a distinct pedicel, overlapping 3–4-seriate, pale to dark brown, broadly fusoid, 7–9-transversally septate ascospores with a vertical septum in nearly all median cells. Multigene phylogenetic analyses, using partial sequences from the 28S nrRNA gene (LSU), 18S nrRNA gene (SSU), internal transcribed spacer regions and intervening 5.8S nrRNA gene (ITS) of the nrDNA operon and the translation elongation factor 1-alpha region (TEF) demonstrated a monophyletic affiliation of the new strain, accommodating the species of Phaeoseptum in the family Phaeoseptaceae. With further morphological and phylogenetic investigations, we justify the new fungus as a novel species, Phaeoseptum hydei in Phaeoseptaceae. Detailed descriptions and illustrations are provided for Phaeoseptum hydei and this novel species compared with the remaining species found in the genus. An updated checklist of microfungi recorded on Delonix regia from around the world is also provided.

scholarly journals Emergence of Prochloraz-Resistant Populations of Calonectria pauciramosa and Calonectria polizzii in Ornamental Nurseries of Southern Italy

Plant Disease ◽  
2014 ◽  
Vol 98 (3) ◽  
pp. 344-350 ◽  
Author(s):  
Vladimiro Guarnaccia ◽  
Dalia Aiello ◽  
Giancarlo Polizzi ◽  
Giancarlo Perrone ◽  
Gaetano Stea ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Red Clover ◽  
Translation Elongation ◽  
Group A ◽  
Sterol Demethylation Inhibitors ◽  
Benzimidazole Carbamates ◽  
Group B ◽  
Translation Elongation Factor 1Α

Management of Calonectria spp. infections in nurseries requires scheduled fungicide applications, particularly with methyl benzimidazole carbamates (MBCs) and sterol demethylation inhibitors (DMIs). Due to rising concerns about the occurrence of MBC resistance in different Calonectria populations and variability in prochloraz efficacy in controlling these pathogens, a detailed study on prochloraz sensitivity distributions of Calonectria isolates belonging to the Calonectria scoparia complex was carried out. In total, 105 isolates collected in two distinct periods (1993 to 1996 and 2005 to 2009) were analyzed for prochloraz sensitivity. Based on DNA sequencing and phylogenetic analyses of β-tubulin, histone H3, and translation elongation factor-1α gene sequences, 69 and 36 isolates were identified as C. pauciramosa and C. polizzii, respectively. The isolates collected more recently (group B) had a reduced prochloraz sensitivity, as indicated by greater values for the effective dose to reduce growth by 50% than those collected earlier (group A). The reduced sensitivity detected in vitro corresponded to partial loss of fungicide efficacy in controlling infections in red clover and feijoa under controlled and semi-field conditions, respectively. Frequent prochloraz application in nurseries for controlling Calonectria spp. infections is discouraged.

scholarly journals Molecular characterization and phylogenetic analyses of Lophodermella needle pathogens (Rhytismataceae) on Pinus species in the USA and Europe

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11435
Author(s):  
Jessa P. Ata ◽  
Kelly S. Burns ◽  
Suzanne Marchetti ◽  
Isabel A. Munck ◽  
Ludwig Beenken ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Ribosomal Subunit ◽  
Elongation Factor ◽  
Translation Elongation ◽  
Phenotypic Characters ◽  
Elongation Factor 1 Alpha ◽  
The Usa ◽  
Phylogenetic Resolution ◽  
Elongation Factor 1

Increasing prevalence of conifer needle pathogens globally have prompted further studies on pathogen identification and a better understanding of phylogenetic relationships among needle pathogens. Several Lophodermella species can be aggressive pathogens causing needle cast in natural pine forests in the USA and Europe. However, their relationships with other Rhytismataceae species have historically been based on similarities of only limited phenotypic characters. Currently, no molecular studies have been completed to elucidate their relationships with other Lophodermella needle pathogens. This study collected and sequenced three gene loci, namely: internal transcribed spacer, large ribosomal subunit, and translation elongation factor 1-alpha, from five Lophodermella needle pathogens from North America (L. arcuata, L. concolor, L. montivaga) and Europe (L. conjuncta and L. sulcigena) to distinguish phylogeny within Rhytismatacaeae, including Lophophacidium dooksii. Phylogenetic analyses of the three loci revealed that all but L. conjuncta that were sampled in this study consistently clustered in a well-supported clade within Rhytismataceae. The multi-gene phylogeny also confirmed consistent nesting of L. dooksii, a needle pathogen of Pinus strobus, within the clade. Potential synapomorphic characters such as ascomata position and ascospore shape for the distinct clade were also explored. Further, a rhytismataceous species on P. flexilis that was morphologically identified as L. arcuata was found to be unique based on the sequences at the three loci. This study suggests a potential wider range of host species within the genus and the need for genetic characterization of other Lophodermella and Lophophacidium species to provide a higher phylogenetic resolution.

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