Morphoanatomical and phylogenetic characterization of the ectomycorrhiza between <em>Laccaria squarrosa</em> with <em>Pinus pseudostrobus</em> and its relevance for reforestation programs

Background: Pinus (Coniferophyta) and Laccaria (Basidiomycota) establish ectomycorrhizal symbioses in natural forests. However, their detailed morphoanatomical and phylogenetic characterization have received little attention. Accurate identification of native host symbionts is of paramount relevance to the production of mycorrhized seedlings for successful reforestation programs. Questions/Objective: We aimed to determine if L. squarrosa is able to establish ectomycorrhizal symbiosis with gymnosperms, thereby widening its host range and highlighting its relevance as a potential inoculant for pine seedlings. Currently, L. squarrosa is only known from its type collection associated with the angiosperm Fagus grandifolia var. mexicana. Studied species: The fungus L. squarrosa and Pinus pseudostrobus, a tree endemic to Mexico. Study site and dates: A Pinus-Quercus forest in Piedra Canteada, Nanacamilpa, Tlaxcala; 2018-2020. Methods: L. squarrosa basidiomata were identified and ectomycorrhizal roots were collected and morphoanatomically characterized. For molecular identification, DNA was extracted, PCR was performed targeting the nuclear ribosomal internal transcribed spacer region (nucrDNA ITS) for the mycobiont identification and the chloroplastic single-locus trnL region for the phytobiont. Results: In the phylogenetic analyses, our sequences from basidiomata and ectomycorrhizae clustered together with L.squarrosa with high values of supporting identity. Meanwhile, P. pseudostrobus was molecularly identified as the phytobiont. Conclusions: This is one of the few worldwide characterizations of Laccaria ectomycorrhiza under field conditions and contributes to the understanding of the ecology, distribution, and economic relevance of the symbiotic association. Our data suggest that L. squarrosa has potential for use as a native inoculant for P. pseudostrobus tree production. Translate stop Translate stop

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Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree

Scientific Reports ◽

10.1038/s41598-021-87886-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Sebastiana ◽

A. Gargallo-Garriga ◽

J. Sardans ◽

M. Pérez-Trujillo ◽

F. Monteiro ◽

...

Keyword(s):

Molecular Mechanisms ◽

Positive Impact ◽

Ectomycorrhizal Fungus ◽

Cork Oak ◽

Mycorrhizal Symbiosis ◽

Gamma Aminobutyric Acid ◽

Ectomycorrhizal Symbiosis ◽

Ectomycorrhizal Roots ◽

Oak Tree ◽

Mycorrhizal Roots

AbstractMycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results show that compounds putatively corresponding to carbohydrates, organic acids, tannins, long-chain fatty acids and monoacylglycerols, were depleted in ectomycorrhizal cork oak colonized roots. Conversely, non-proteogenic amino acids, such as gamma-aminobutyric acid (GABA), and several putative defense-related compounds, including oxylipin-family compounds, terpenoids and B6 vitamers were induced in mycorrhizal roots. Transcriptomic analysis suggests the involvement of GABA in ectomycorrhizal symbiosis through increased synthesis and inhibition of degradation in mycorrhizal roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.

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Yeast Species Associated with Orange Juice: Evaluation of Different Identification Methods

Applied and Environmental Microbiology ◽

10.1128/aem.68.4.1955-1961.2002 ◽

2002 ◽

Vol 68 (4) ◽

pp. 1955-1961 ◽

Cited By ~ 87

Author(s):

Covadonga R. Arias ◽

Jacqueline K. Burns ◽

Lorrie M. Friedrich ◽

Renee M. Goodrich ◽

Mickey E. Parish

Keyword(s):

Orange Juice ◽

Restriction Pattern ◽

Partial Sequence ◽

Rrna Gene ◽

Correct Identification ◽

Internal Transcribed Spacer Region ◽

Accurate Identification ◽

Hanseniaspora Uvarum ◽

Classical Methodology ◽

26S Rrna

ABSTRACT Five different methods were used to identify yeast isolates from a variety of citrus juice sources. A total of 99 strains, including reference strains, were identified using a partial sequence of the 26S rRNA gene, restriction pattern analysis of the internal transcribed spacer region (5.8S-ITS), classical methodology, the RapID Yeast Plus system, and API 20C AUX. Twenty-three different species were identified representing 11 different genera. Distribution of the species was considerably different depending on the type of sample. Fourteen different species were identified from pasteurized single-strength orange juice that had been contaminated after pasteurization (PSOJ), while only six species were isolated from fresh-squeezed, unpasteurized orange juice (FSOJ). Among PSOJ isolates, Candida intermedia and Candida parapsilosis were the predominant species. Hanseniaspora occidentalis and Hanseniaspora uvarum represented up to 73% of total FSOJ isolates. Partial sequence of the 26S rRNA gene yielded the best results in terms of correct identification, followed by classical techniques and 5.8S-ITS analysis. The commercial identification kits RapID Yeast Plus system and API 20C AUX were able to correctly identify only 35 and 13% of the isolates, respectively. Six new 5.8S-ITS profiles were described, corresponding to Clavispora lusitaniae, Geotrichum citri-aurantii, H. occidentalis, H. vineae, Pichia fermentans, and Saccharomycopsis crataegensis. With the addition of these new profiles to the existing database, the use of 5.8S-ITS sequence became the best tool for rapid and accurate identification of yeast isolates from orange juice.

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Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

10.21203/rs.3.rs-289731/v1 ◽

2021 ◽

Author(s):

Blessing Amaka Ezeonuegbu ◽

Dauda Abdullahi Machido ◽

Clement Z. Whong ◽

Wisdom S. Japhet ◽

Clement Ameh Yaro ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Industrial Effluent ◽

Pcr Amplification ◽

Morphological Characterization ◽

Likelihood Method ◽

Internal Transcribed Spacer Region ◽

Fungal Isolates ◽

Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

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Eutypa, Eutypella, and Cryptovalsa Species (Diatrypaceae) Associated with Prunus Species in South Africa

Plant Disease ◽

10.1094/pdis-11-17-1696-re ◽

2018 ◽

Vol 102 (7) ◽

pp. 1402-1409 ◽

Cited By ~ 4

Author(s):

Providence Moyo ◽

Ulrike Damm ◽

Lizel Mostert ◽

Francois Halleen

Keyword(s):

South Africa ◽

Phylogenetic Analyses ◽

Fruit Trees ◽

Fungal Species ◽

Stone Fruit ◽

Prunus Species ◽

Internal Transcribed Spacer Region ◽

Eutypa Lata ◽

Eutypa Dieback ◽

Prunus Spp

Stone fruit trees (Prunus spp.) are economically important fruit trees cultivated in South Africa. These trees are often grown in close proximity to vineyards and are to a large extent affected by the same trunk disease pathogens as grapevines. The aim of the present study was to determine whether stone fruit trees are inhabited by Diatrypaceae species known from grapevines and whether these trees could act as alternative hosts for these fungal species. Isolations were carried out from symptomatic wood of Prunus species (almond, apricot, cherry, nectarine, peach, and plum) in stone fruit growing areas in South Africa. Identification of isolates was based on phylogenetic analyses of the internal transcribed spacer region and β-tubulin gene. Forty-six Diatrypaceae isolates were obtained from a total of 380 wood samples, from which five species were identified. All five species have also been associated with dieback of grapevine. The highest number of isolates was found on apricot followed by plum. No Diatrypaceae species were isolated from peach and nectarine. Eutypa lata was the dominant species isolated (26 isolates), followed by Cryptovalsa ampelina (7), Eutypa cremea (5), Eutypella citricola (5), and Eutypella microtheca (3). First reports from Prunus spp. are E. cremea, E. citricola, and E. microtheca. Pathogenicity tests conducted on apricot and plum revealed that all these species are pathogenic to these hosts, causing red-brown necrotic lesions like those typical of Eutypa dieback on apricot.

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Amanita submelleialba sp. nov. in section Amanita from northern Thailand

Phytotaxa ◽

10.11646/phytotaxa.513.2.4 ◽

2021 ◽

Vol 513 (2) ◽

pp. 129-140

Author(s):

YUAN S. LIU ◽

JIAN-KUI LIU ◽

PETER E. MORTIMER ◽

SAISAMORN LUMYONG

Keyword(s):

Rna Polymerase Ii ◽

Phylogenetic Analyses ◽

Line Drawing ◽

Elongation Factor ◽

Morphological Characteristics ◽

Nuclear Rdna ◽

Internal Transcribed Spacer Region ◽

Northern Thailand ◽

Extant Species ◽

Distinct Lineage

Amanita submelleialba sp. nov. in section Amanita, is described from northern Thailand based on both multi-gene phylogenetic analysis and morphological evidences. It is characterized by having small to medium-sized basidiomata; a yellow to yellowish pale pileus covering pyramidal to subconical, white to yellow white volval remnants; globose stipe base covered conical, white to yellow white volval remnants; fugacious subapical annulus; and absent clamps. Multi-gene phylogenetic analyses based on partial nuclear rDNA internal transcribed spacer region (ITS), partial nuclear rDNA larger subunit region (nrLSU), RNA polymerase II second largest subunit (RPB2), partial translation elongation factor 1-alpha (TEF1-α) and beta-tubulin gene (TUB) indicated that A. submelleialba clustered together with A. elata and A. mira, but represented as a distinct lineage from other extant species in section Amanita. The detailed morphological characteristics, line-drawing illustration and comparisons with morphologically similar taxa are provided.

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Phylogenetic Characterization of Arboviruses in Patients Suffering from Acute Fever in Rondônia, Brazil

Viruses ◽

10.3390/v12080889 ◽

2020 ◽

Vol 12 (8) ◽

pp. 889

Author(s):

Jackson Alves da Silva Queiroz ◽

Luan Felipo Botelho-Souza ◽

Felipe Souza Nogueira-Lima ◽

Rita de Cássia Pontello Rampazzo ◽

Marco Aurélio Krieger ◽

...

Keyword(s):

Viral Load ◽

Phylogenetic Analyses ◽

Metropolitan Region ◽

Evolutionary Analysis ◽

Detectable Viral Load ◽

Conventional Pcr ◽

Serum Samples ◽

Phylogenetic Characterization ◽

Genotype V ◽

Genotype Ii

The purpose of the study was to classify, through phylogenetic analyses, the main arboviruses that have been isolated in the metropolitan region of Porto Velho, Rondônia, Brazil. Serum samples from patients with symptoms suggesting arboviruses were collected and tested by One Step RT-qPCR for Zika, Dengue (serotypes 1–4), Chikungunya, Mayaro and Oropouche viruses. Positive samples were amplified by conventional PCR and sequenced utilizing the Sanger method. The obtained sequences were aligned, and an evolutionary analysis was carried out using Bayesian inference. A total of 308 samples were tested. Of this total, 20 had a detectable viral load for Dengue, being detected DENV1 (18/20), co-infection DENV1 and DENV2 (1/20) and DENV4 (1/20). For Dengue serotype 3 and for the CHIKV, ZIKV, MAYV and OROV viruses, no individuals with a detectable viral load were found. A total of 9 of these samples were magnified by conventional PCR for sequencing. Of these, 6 were successfully sequenced and, according to the evolutionary profile, 5 corresponded to serotype DENV-1 genotype V, and 1 to serotype DENV-4 genotype II. In the study, we demonstrate co-circulation of the DENV-1 genotype V and the DENV-4 genotype II. Co-circulation of several DENV serotypes in the same city poses a risk to the population and is correlated with the increase of the most severe forms of the disease. Similarly, co-circulation of genetically distinct DENV and the occurrence of simultaneous infections can affect recombination events and lead to the emergence of more virulent isolates.

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Tree kangaroo molecular systematics based on partial cytochrome b sequences: are Matschie's tree kangaroo (Dendrolagus matschiei) and Goodfellow's tree kangaroo (D. goodfellowi buergersi) sister taxa?

Australian Mammalogy ◽

10.1071/am10017 ◽

2012 ◽

Vol 34 (1) ◽

pp. 18 ◽

Cited By ~ 3

Author(s):

Thomas J. McGreevy ◽

Lisa Dabek ◽

Thomas P. Husband

Keyword(s):

Mitochondrial Dna ◽

Papua New Guinea ◽

Cytochrome B ◽

Molecular Systematics ◽

Phylogenetic Analyses ◽

New Guinea ◽

Critically Endangered ◽

Evolutionary Relationships ◽

Accurate Identification ◽

Identification Of Species

New Guinea tree kangaroos (Dendrolagus spp.) are unique arboreal macropodid marsupials mainly listed as critically endangered or endangered. The molecular systematics of Dendrolagus has not been fully resolved and is critical for the accurate identification of species and their evolutionary relationships. Matschie’s tree kangaroo (D. matschiei) and Goodfellow’s tree kangaroo (D. goodfellowi buergersi) share numerous morphological, physiological, and behavioural traits. We analysed the partial mitochondrial DNA cytochrome b gene for D. matschiei (n = 67), D. g. buergersi (n = 8), D. goodfellowi unidentified ssp. (n = 8), golden-mantled tree kangaroo (D. g. pulcherrimus; n = 1), and two additional New Guinea Dendrolagus taxa to determine whether D. matschiei and D. g. buergersi are sister taxa. D. matschiei and D. g. buergersi were not placed as sister taxa in our phylogenetic analyses; however, we were unable to analyse a known sample from a D. g. goodfellowi. We found initial genetic evidence that D. matschiei and the Lowland tree kangaroo (D. spadix) are sister taxa – they may have diverged after the formation of the Huon Peninsula of Papua New Guinea. Our results also support the elevation of D. g. pulcherrimus to a full species. An improved understanding of Dendrolagus molecular systematics will contribute substantially to their conservation.

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A new Crocus L. (Iridaceae) species from SE Turkey, based on morphological and molecular data

Phytotaxa ◽

10.11646/phytotaxa.239.3.3 ◽

2015 ◽

Vol 239 (3) ◽

pp. 223 ◽

Cited By ~ 1

Author(s):

Osman Erol ◽

Doerte Harpke ◽

Hasan Yıldırım

Keyword(s):

Phylogenetic Analyses ◽

Type Specimen ◽

Morphological Characters ◽

Molecular Data ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Position ◽

Full Description ◽

New Taxon ◽

Internal Transcribed Spacer Region ◽

Se Turkey

Crocus musagecitii is described as a new species. Diagnostic morphological characters, a full description and detailed illustrations are provided on the basis of the type specimen and wild specimens. Morphologically, C. musagecitii is close to Crocus biflorus subsp. pseudonubigena. Crocus musagecitii differs from C. biflorus subsp. pseudonubigena by the lack of stripes or narrow purplish tongue on outside of outer tepals, wider tepals, and homogenously yellow anthers. In order to clarify the phylogenetic position of this species within the Crocus adamii species complex, we sequenced the internal transcribed spacer region (ITS: ITS1 + 5.8SrDNA + ITS2) and 5’ external transcribed spacer (ETS) of the nuclear ribosomal DNA (rDNA). A phylogenetic tree obtained by Bayesian phylogenetic inference is given. Phylogenetic analyses revealed that the new taxon is close to C. munzurensis. Crocus musagecitii differs from its phylogenetically closest relative C. munzurensis by the corm tunics (C. musagecitii: coriaceus; C. munzurensis: membranous), the number of leaves (C. musagecitii: up to 8; C. munzurensis: up to 4) and non-hairy leaf margins.

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Diversity of Diatrypaceae Species Associated with Dieback of Grapevines in South Africa, with the Description of Eutypa cremea sp. nov.

Plant Disease ◽

10.1094/pdis-05-17-0738-re ◽

2018 ◽

Vol 102 (1) ◽

pp. 220-230 ◽

Cited By ~ 6

Author(s):

Providence Moyo ◽

Lizel Mostert ◽

Christoffel F.J. Spies ◽

Ulrike Damm ◽

Francois Halleen

Keyword(s):

South Africa ◽

Cross Section ◽

Internal Transcribed Spacer ◽

Dominant Species ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Internal Transcribed Spacer Region ◽

Canker Pathogen ◽

Grapevine Canker ◽

First Time

Recent studies in grape-growing areas including Australia, California, and Spain have revealed an extensive diversity of Diatrypaceae species on grapevines showing dieback symptoms and cankers. However, in South Africa, little is known regarding the diversity of these species in vineyards. The aim of this study was, therefore, to identify and characterize Diatrypaceae species associated with dieback symptoms of grapevine in South Africa. Isolates were collected from dying spurs of grapevines aged 4 to 8 years old, grapevine wood showing wedge-shaped necrosis when cut in cross section as well as from perithecia on dead grapevine wood. The collected isolates were identified based on morphological characters and phylogenetic analyses of the internal transcribed spacer region (ITS) and β-tubulin gene. Seven Diatrypaceae species were identified on grapevine, namely Cryptovalsa ampelina, C. rabenhorstii, Eutypa consobrina, E. lata, E. cremea sp. nov., Eutypella citricola, and E. microtheca. The dying spurs yielded the highest diversity of species when compared with the wedge-shaped necrosis and/or perithecia. C. ampelina was the dominant species in the dying spurs, followed by E. citricola, whereas E. lata was the dominant species isolated from the wedge-shaped necroses and perithecia. These results confirm E. lata as an important grapevine canker pathogen in South Africa, but the frequent association of C. ampelina with spur dieback suggests that this pathogen plays a more prominent role in dieback than previously assumed. In some cases, more than one species were isolated from a single symptom, which suggests that interactions may be occurring leading to decline of grapevines. C. rabenhorstii, E. consobrina, E. citricola, E. microtheca, and E. cremea are reported for the first time on grapevine in South Africa.

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A new concept for Dictyostelium sphaerocephalum based on morphology and phylogenetic analysis of nuclear ribosomal internal transcribed spacer region sequences

Canadian Journal of Botany ◽

10.1139/b06-147 ◽

2007 ◽

Vol 85 (1) ◽

pp. 104-110 ◽

Cited By ~ 2

Author(s):

Maria Romeralo ◽

Omar Fiz-Palacios ◽

Carlos Lado ◽

James C. Cavender

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Morphological Plasticity ◽

Branching Pattern ◽

Classical Concept ◽

Internal Transcribed Spacer Region

Three dictyostelid isolates were found in Spain and Argentina that are morphologically different from known species. These isolates have some features similar to Dictyostelium sphaerocephalum (Oudem.) Sacc., Marchal & É.J. Marchal, but differ in size and sorocarp branching pattern. We sequenced the nuclear ribosomal internal transcribed spacer region to explore phylogenetic relationships among this group of species, including the three new isolates and their closest relatives. In all phylogenetic analyses performed, sequences of all three isolates group together with sequences from “typical” D. sphaerocephalum samples. This result supports previous observations of the morphological plasticity in dictyostelids, especially D. sphaerocephalum, leading us to broaden the classical concept of this species.

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