scholarly journals Taxonomic evaluation of selected Ganoderma species and database sequence validation

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3596 ◽  
Author(s):  
Suldbold Jargalmaa ◽  
John A. Eimes ◽  
Myung Soo Park ◽  
Jae Young Park ◽  
Seung-Yoon Oh ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Economic Value ◽  
Elongation Factor ◽  
Distribution Patterns ◽  
Fungal Species ◽  
Morphological Features ◽  
Bootstrap Support ◽  
Translation Elongation ◽  
Identification Of Species ◽  
High Bootstrap

Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II). These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species.

scholarly journals Dieback of Euonymus alatus (Celastraceae) Caused by Cytospora haidianensis sp. nov. in China

Forests ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 524 ◽  
Author(s):  
Xian Zhou ◽  
Meng Pan ◽  
Haoyu Li ◽  
Chengming Tian ◽  
Xinlei Fan
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Economic Value ◽  
Carbon Sources ◽  
Elongation Factor ◽  
Causal Agent ◽  
Optimum Growth ◽  
Translation Elongation ◽  
Euonymus Alatus ◽  
Pathogenicity Tests

Euonymus alatus (Celastraceae) is widely cultivated in China for its economic value and landscape benefits. Euonymus alatus dieback occurs due to members of Cytospora and has become one of the most severe diseases affecting its cultivation in China. In this study, we examined the causal agent of bough dieback on campuses of University Road, Beijing, China. Among the strains, three were morphologically consistent with Cytospora, showing hyaline and allantoid conidia. Based on phylogenetic analyses of the concatenated actin (ACT), internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), translation elongation factor 1-alpha (TEF1-α) and beta-tubulin (TUB2) gene sequences, along with morphological and physiological features, we propose C. haidianensis as a novel species. It was confirmed as a causal agent of dieback of E. alatus by pathogenicity tests. Mycelial growth of Cytospora haidianensis occurred at pH values ranging from 3.0 to 11.0, with optimum growth at 8.3, and at temperatures from 5 to 35 °C, with optimum growth at 19.8 °C. We also tested the growth of C. haidianensis in the presence of six carbon sources. Sucrose, maltose and glucose were highly efficient and xylose was the least. The ability of C. haidianensis to grow at 19.8 °C may help to explain its occurrence causing dieback of E. alatus in Beijing during the autumn season.

scholarly journals Stem Blight of Blueberry Caused by Lasiodiplodia vaccinii sp. nov. in China

Plant Disease ◽  
2019 ◽  
Vol 103 (8) ◽  
pp. 2041-2050 ◽  
Author(s):  
Lin Zhao ◽  
Yu Wang ◽  
Wei He ◽  
Ying Zhang
Keyword(s):  
Rna Polymerase Ii ◽  
Mycelial Growth ◽  
Economic Value ◽  
Carbon Sources ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Nitrogen Sources ◽  
Fungal Species ◽  
Stem Blight ◽  
Nutritional Benefits

Blueberries (Vaccinium spp.) are largely cultivated in China because of their nutritional benefits and economic value. Blueberry stem blight caused by members of the Botryosphaeriaceae has become one of the most severe diseases affecting blueberry cultivation in China. In this study, we examined the causal agent of blueberry stem blight at commercial greenhouse farms in the suburban area of Beijing, China. In total, 37 isolates of Botryosphaeriaceae were obtained from 100 stem blight samples of blueberry. Twelve of 37 strains were morphologically consistent with the genus Lasiodiplodia, showing ellipsoid to ovoid, one-celled, hyaline conidia that sometimes turned brown, with median septa and longitudinal striations when mature. These 12 strains were identified as belonging to a novel fungal species, Lasiodiplodia vaccinii, based on phylogenetic analysis of the concatenated internal transcribed spacer, RNA polymerase II gene, β-tubulin gene, and translation elongation factor-1α gene sequences as well as morphological characteristics. Pathogenicity tests indicated that L. vaccinii can cause twig blight on blueberry seedlings in the greenhouse. Mycelial growth of L. vaccinii occurred at pH values ranging from 3.0 to 10.0, with an optimum at 6.2, and at temperatures from 15 to 40°C, with an optimum at 30.3°C. Of the seven carbon sources tested, sucrose, fructose, and glucose were all highly efficient in supporting the mycelial growth of L. vaccinii, and xylose was the least effective. Of six nitrogen sources tested, yeast extract and tryptone best promoted mycelial growth of L. vaccinii. The ability of L. vaccinii to grow at high temperatures may help to explain its occurrence in Beijing greenhouses in this study.

scholarly journals A new species of Balansia (Clavicipitaceae) associated with a cyperaceous plant in Brazil

2021 ◽  
Author(s):  
Debora Guterres ◽  
Roberto Ramos-Sobrinho ◽  
Danilo B. Pinho ◽  
Iraildes P. Assunção ◽  
Gaus S.A. Lima
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Ribosomal Dna ◽  
Elongation Factor ◽  
Molecular Data ◽  
Fungal Species ◽  
Internal Transcribed Spacers ◽  
Translation Elongation ◽  
Elongation Factor 1 ◽  
A New Species

Abstract Fungal species belonging to the genus Balansia (Clavicipitaceae) are well known as endophytic and epibiotic species commonly found on grasses or sedges. Among the 36 species of Balansia described worldwide, ten have been reported in Brazil. While most species of balansoid fungi were described on graminaceous plants, only four were characterized on cyperaceous hosts. To correctly identify the species of balansoid fungi associated with Scleria bracteata (Cyperaceae), specimens were collected in the state of Alagoas, Brazil, in 2014 and 2016. Nucleotide partial sequences of the second-largest subunit of RNA polymerase II (RPB2), translation elongation factor 1-α (TEF1), 18S subunit ribosomal DNA (SSU), 28S subunit ribosomal DNA (LSU), and internal transcribed spacers (ITS) were obtained from each balansoid specimen. Based on morphology and molecular data, the specimens were identified as a putative new species of Balansia, herein referred to as Balansia scleriae sp. nov.

scholarly journals Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision

2018 ◽  
Vol 63 (2) ◽  
pp. 45-64 ◽  
Author(s):  
Jolanta Miadlikowska ◽  
Nicolas Magain ◽  
Carlos J. Pardo-De la Hoz ◽  
Dongling Niu ◽  
Trevor Goward ◽  
...  
Keyword(s):  
High Specificity ◽  
Molecular Data ◽  
Fungal Species ◽  
Bootstrap Support ◽  
Phenotypic Traits ◽  
Phylogenetic Structure ◽  
Putative Species ◽  
Molecular Phylogenetic ◽  
High Bootstrap ◽  
Phylogenetic Revision

AbstractClosely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.

Identification of Pathogenic Fusarium spp. Responsible for Root Rot of Angelica sinensis and Characterization of their Biological Enemies in Dingxi, China

Plant Disease ◽  
2022 ◽  
Author(s):  
Liu Yang ◽  
Tian Yuan ◽  
Xia Zhao ◽  
Yue Liang ◽  
UWAREMWE CONSTANTINE ◽  
...  
Keyword(s):  
Root Rot ◽  
Elongation Factor ◽  
Its Region ◽  
Fungal Species ◽  
Cortical Cells ◽  
Translation Elongation ◽  
Field Samples ◽  
Fusarium Pathogens ◽  
Rot Disease ◽  
Serious Disease

Root rot is a serious disease in plantations of A. sinensis, severely affecting yield and quality and threatening sustainable production. Fusarium isolates (n=32) were obtained from field samples of root rot tissue, leaves and infected soil. Isolates were identified by comparing the sequences of their internal transcribed spacer (ITS) region and translation elongation factor 1-ɑ (TEF-1ɑ) to sequences of known species in the NCBI-database. These Fusarium isolates include F. tricinctum (43.75%), F. equiseti (31.25%), F. solani (9.37%), F. oxysporum (6.25%), F. acuminatum (6.25%), and F. incarnatum (3.12%). For pathogenicity testing under greenhouse conditions, seven isolates were selected based on a phylogenetic analysis, including four strains of F. tricinctum and one strain each of F. solani, F. oxysporum, and F. acuminatum. The seven isolates were all pathogenic but differed in their ability to infect: the four F. tricinctum strains were capable pathogens causing root rot in A. sinensis at 100% incidence and the highly aggressive. Furthermore, the symptoms of root rot induced by those seven isolates were consistent with typical root rot cases in the field, but their disease severity varied. Observed histopathological preparations of F. tricinctum-infected seedlings and tissue-slides results showed this fungal species can penetrate epidermal cells and colonize the cortical cells where it induces necrosis and severe plasmolysis. Plate confrontation experiments showed that isolated rhizosphere bacteria inhibited the Fusarium pathogens that cause root rot in A. sinensis. Our results provide timely information for informing the use of biocontrol agents for suppression of root rot disease.

scholarly journals Fusarium incarnatum-equiseti complex from China

2019 ◽  
Vol 43 (1) ◽  
pp. 70-89 ◽  
Author(s):  
M.M. Wang ◽  
Q. Chen ◽  
Y.Z. Diao ◽  
W.J. Duan ◽  
L. Cai
Keyword(s):  
Rna Polymerase ◽  
Elongation Factor ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Ribosomal Gene ◽  
Internal Transcribed Spacers ◽  
Translation Elongation ◽  
Cultural Methods ◽  
Wide Range

The Fusarium incarnatum-equiseti species complex (FIESC) is shown to encompass 33 phylogenetic species, across a wide range of habitats/hosts around the world. Here, 77 pathogenic and endophytic FIESC strains collected from China were studied to investigate the phylogenetic relationships within FIESC, based on a polyphasic approach combining morphological characters, multi-locus phylogeny and distribution patterns. The importance of standardised cultural methods to the identification and classification of taxa in the FIESC is highlighted. Morphological features of macroconidia, including the shape, size and septum number, were considered as diagnostic characters within the FIESC. A multi-locus dataset encompassing the 5.8S nuclear ribosomal gene with the two flanking internal transcribed spacers (ITS), translation elongation factor (EF-1α), calmodulin (CAM), partial RNA polymerase largest subunit (RPB1) and partial RNA polymerase second largest subunit (RPB2), was generated to distinguish species within the FIESC. Nine novel species were identified and described. The RPB2 locus is demonstrated to be a primary barcode with high success rate in amplification, and to have the best species delimitation compared to the other four tested loci.

Morphological characters and phylogenetic analysis reveal a new species of Phellinus with hooked hymenial setae from Vietnam

Phytotaxa ◽  
2018 ◽  
Vol 356 (1) ◽  
pp. 91 ◽  
Author(s):  
LIN ZHU ◽  
XING JI ◽  
JING SI ◽  
BAO-KAI CUI
Keyword(s):  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characters ◽  
Molecular Data ◽  
Translation Elongation ◽  
The Status ◽  
Large Subunit Rdna ◽  
Elongation Factor 1 ◽  
A New Species

Phellinus vietnamensis sp. nov. is described from Vietnam based on morphological characters and molecular data. Morphologically, it is characterized by perennial, pileate basidiomata, a dimitic hyphal system, hooked hymenial setae, and colorless, broadly subglobose to ovoid, thick-walled basidiospores 5.5–6 × 4.8–5.2 μm. Phylogenetically, the status of Phellinus vietnamensis is strongly supported based on sequences of the nuclear internal transcribed spacer (ITS) regions, the translation elongation factor 1-α gene (EF1-α) nuclear large subunit rDNA (nrLSU) and the second largest subunits of RNA polymerase II (RPB2).

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.

scholarly journals Identification of Species in the Botryosphaeriaceae Family Causing Stem Blight on Southern Highbush Blueberry in Florida

Plant Disease ◽  
2010 ◽  
Vol 94 (8) ◽  
pp. 966-971 ◽  
Author(s):  
A. F. Wright ◽  
P. F. Harmon
Keyword(s):  
Population Change ◽  
Elongation Factor ◽  
Fungal Species ◽  
Highbush Blueberry ◽  
Internal Transcribed Spacer Region ◽  
Stem Blight ◽  
The Family ◽  
Identification Of Species ◽  
Time Of Year ◽  
Southern Highbush

Stem blight of southern highbush blueberry (SHB) results in premature plant mortality and has been identified by Florida blueberry growers as the economically most important disease for the industry. In 2007, plants with stem blight and dieback symptoms were sampled at 4-month intervals from two farms located in Alachua and Polk Co., FL. In all, 30 cane samples (stem blight) and 30 crown segments (dieback) were collected at each sample date and each location. In total, 360 samples were collected; fungal species in the family Botryosphaeriaceae were isolated from 85% of the samples. Based on morphology and phylogenetic analysis of the internal transcribed spacer region and elongation factor 1-α (EF1-α) sequences, two dominant species recovered from SHB in Florida were identified: Lasiodiplodia theobromae and Neofusicoccum ribis. Species isolation was independent of location, symptom type, and time of year. Additional samplings are needed to investigate population change over multiple years and in the rest of the southeastern United States. Breeding for resistance and management of stem blight and dieback in Florida should focus on these two fungal species.

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