Sequence Analysis of SSR-Flanking Regions Identifies Genome Affinities between Pasture Grass Fungal Endophyte Taxa

Fungal species of the Neotyphodium and Epichloë genera are endophytes of pasture grasses showing complex differences of life-cycle and genetic architecture. Simple sequence repeat (SSR) markers have been developed from endophyte-derived expressed sequence tag (EST) collections. Although SSR array size polymorphisms are appropriate for phenetic analysis to distinguish between taxa, the capacity to resolve phylogenetic relationships is limited by both homoplasy and heteroploidy effects. In contrast, nonrepetitive sequence regions that flank SSRs have been effectively implemented in this study to demonstrate a common evolutionary origin of grass fungal endophytes. Consistent patterns of relationships between specific taxa were apparent across multiple target loci, confirming previous studies of genome evolution based on variation of individual genes. Evidence was obtained for the definition of endophyte taxa not only through genomic affinities but also by relative gene content. Results were compatible with the current view that some asexual Neotyphodium species arose following interspecific hybridisation between sexual Epichloë ancestors. Phylogenetic analysis of SSR-flanking regions, in combination with the results of previous studies with other EST-derived SSR markers, further permitted characterisation of Neotyphodium isolates that could not be assigned to known taxa on the basis of morphological characteristics.

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Temporal variations in isolation frequency of endophytic fungi of Japanese beech

Canadian Journal of Botany ◽

10.1139/b98-220 ◽

1999 ◽

Vol 77 (2) ◽

pp. 197-202 ◽

Cited By ~ 5

Author(s):

Norio Sahashi ◽

Takanori Kubono ◽

Yukiko Miyasawa ◽

Shin'ichiro Ito

Keyword(s):

Fungal Endophytes ◽

Temporal Variations ◽

Fungal Endophyte ◽

Fagus Crenata ◽

Fungal Species ◽

Organ Specificity ◽

Japanese Beech ◽

Isolation Frequency ◽

Specific Distribution ◽

Unidentified Species

To determine the dominant fungal endophytes of the Japanese beech (Fagus crenata Blume) and to monitor their isolation frequency, we isolated fungi from symptomless organs of beech including leaves, petioles, and current and old (1- to 5-year-old) twigs after surface sterilization. Of the 13 fungal taxa obtained, 3 were isolated most often. An unidentified species of Discula and an unidentified sterile fungus, Lb, were isolated frequently from leaves, and an unidentified species of Phomopsis was isolated most frequently from twigs. The isolation frequency over the growing season varied for the two dominant fungal species in the leaves, Discula sp. and Lb. These two species had similar patterns of isolation, even in petioles and current-year twigs, although isolation frequencies of a given species varied with organs. An organ-specific distribution of the fungal species in the host plant was apparent. The three fungal species noted above were considered to be the dominant endophytes of the Japanese beech.Key words: fungal endophyte, Fagus crenata, isolation frequency, organ specificity.

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Biodiversity study of endophytic fungi associated with two Quercus species in Iran

Forest Systems ◽

10.5424/fs/2019281-14528 ◽

2019 ◽

Vol 28 (1) ◽

pp. e003

Author(s):

Saied Ghasemi ◽

Sima Khodaei ◽

Kaivan Karimi ◽

Majid Tavakoli ◽

Illaria Pertot ◽

...

Keyword(s):

Endophytic Fungi ◽

Fungal Endophytes ◽

Morphological Characteristics ◽

Fungal Endophyte ◽

Culture Collection ◽

Its Rdna ◽

Chi Square ◽

Quercus Species ◽

Chi Square Test ◽

East Azerbaijan

Aim of study: In this study, frequency and diversity of fungal endophyte communities inhabiting twigs and branches of apparently healthy Q. macranthera and Q. brantii in East Azerbaijan and Lorestan provinces of Iran is presented.Area of study: East Azerbaijan and Lorestan provinces in Iran.Materials and methods: Culturable fungal endophytes were recovered from wood tissues using routine technique for isolation of fungal endophytes. The identity of fungal isolates were determined based on morphological characteristics and sequences data of ITS-rDNA region and Beta-tubulin gene. Frequency and diversity among fungal communities were analyzed using chi-square test and biodiversity indices.Main results: The highest frequency and diversity was detected for fungal endophyte community recovered from Q. macranthera and East Azerbaijan province. The assemblage of endophytic fungi characterized in this study in healthy tissues of oak trees indicates that some of the fungi are possible latent pathogens such as Biscogniauxia mediterranea with 18.28% frequency followed by Alternaria alternata and Trichothecium roseum respectively. Two fungal taxa of Pyronema domesticum and Valsa persoonii are reported for the first time in Iran. Overall, the results of this study show that the plant species and growth location influence frequency and diversity of culturable fungal endophytic communities of Quercus in Iran.Keywords: Quercus macranthera, Quercus brantii, Fungal endophytes, Molecular identification.Abbreviations used: CBS (Centraal Bureau voor Schimmelcultures); CCTU (Culture Collection of University of Tabriz); GTR (General Time Reversible); HKY (Hasegawa Kishino Yano); ITS-rDNA (Internal Transcribed Space); km (kilometer) ; PDA (Potato Dextrose Agar); TUB (Tubulin).

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New Taxon of Fungal Endophytes from Phrynium capitatum Willd: A Promising Ethnomedicinal Plant in Northeast India and its Systematic and Phylogenetic Analysis

Science & Technology Journal ◽

10.22232/stj.2019.07.01.04 ◽

2019 ◽

Vol 7 (1) ◽

pp. 29-36

Author(s):

Richa Sharma ◽

◽

Sumpam Tangjang ◽

Amritesh C. Shukla ◽

Keyword(s):

Phylogenetic Analysis ◽

Fungal Endophytes ◽

Northeast India ◽

Fungal Endophyte ◽

Fungal Species ◽

New Taxon ◽

Plant Parts ◽

Analgesic Effects ◽

Ethnomedicinal Plant ◽

Pestalotiopsis Neglecta

The findings of the current study deal with the first time report on the diversity of fungal endophyte from the ethnomedicinal plant- Phrynium capitatum Willd., (Marantaceae). The plant is growing wildly in the forest of Papum Pare, Arunachal Pradesh, India, and traditionally been used for anti-diabetic, antihyperglycemic or analgesic effects. During the investigation, samples of the plant parts, viz., leaves, stem, and roots were collected for isolation of endophytic spp. The endophytic spp were identified based on the morphological, cultural, and reproductive structures (hyaline, ellipsoidal, aseptate, pycnidia, beta conidia, perithecia, asci, and ascospores). Further, the phylogenetic analysis of the isolated species was made, using the sequences of 5.8S and 28S rDNA internal transcribed spacer sequence 1 and 4. The largest number of fungal endophytes (39%) were isolated from the leaves, followed by the roots (31%) and stems (30%). Overall 35 fungal species have been isolated, out of which, thirty-four belongs to the class Ascomycetes, and one from the class zygomycetes. The highest species richness and frequency of colonization were recorded in the leaf. The observations show that Pestalotiopsis longiseta was the most dominant endophytic species followed by Diplodina microsperma, Nodulisporium hinnuleum, Aspergillus flavus , Diaporthe sp., Nigrospora oryzae and Lasiodiplodia viticola. However, Pestalotiopsis neglecta, Sordaria fimicola, Diplodina microsperma, Fusarium incarnatum, Preussia sp., Diaporthe sp., Aureobasidium sp.were common fungal endophytes isolated from P. capitatum

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Detection and characterisation of novel fungal endophyte genotypic variation in cultivars of perennial ryegrass (Lolium perenne L.)

Australian Journal of Agricultural Research ◽

10.1071/ar07270 ◽

2008 ◽

Vol 59 (3) ◽

pp. 214 ◽

Cited By ~ 24

Author(s):

E. van Zijll de Jong ◽

M. P. Dobrowolski ◽

A. Sandford ◽

K. F. Smith ◽

M. J. Willocks ◽

...

Keyword(s):

Perennial Ryegrass ◽

Expressed Sequence Tag ◽

Genotypic Variation ◽

Fungal Endophyte ◽

In Planta ◽

Pasture Grass ◽

Grass Endophyte ◽

Incomplete Removal ◽

Genotypic Analysis ◽

Mammalian Herbivore

Alkaloids produced by the perennial ryegrass pasture and turf grass endophyte Neotyphodium lolii confer both beneficial (insect feeding deterrence) and deleterious (mammalian herbivore toxicoses) effects. Novel endophyte strains with altered and desirable in planta metabolic profiles have been introduced into cultivars by inoculation. The potentially severe effects of contamination with standard toxic endophytes provide an important incentive for quality control during varietal development. Genotyping with expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers in order to monitor endophyte content was evaluated in this study. The NEA2 endophyte, described as producing low levels of lolitrem B and moderate quantities of ergovaline and peramine, has been deployed in the cultivar (cv.) Tolosa and transferred to other proprietary varieties by crossing or controlled inoculation. In planta genotypic analysis of cv. Tolosa-derived plants revealed the presence of 2 distinct NEA2 genotypes (A and B). Variable proportions of NEA2 A and B were observed at different stages of cultivar multiplication, and NEA2 B was present in inoculated varieties. Several accessions also revealed the presence of a third genotype (C), identical to standard toxic types. Alkaloid measurement in plants containing individual A and B endophytes identified distinct profiles which collectively account for the average NEA2 profile. The C variant is apparently a contaminant arising from seed or adventitious seedlings during varietal multiplication or incomplete removal of endophyte from seed before inoculation. SSR-based genotyping provides an efficient means to continuously assess endophyte prevalence and identity in pasture grass breeding programs.

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Fungal endophyte assemblages from ethnopharmaceutically important medicinal trees

Canadian Journal of Microbiology ◽

10.1139/w05-143 ◽

2006 ◽

Vol 52 (5) ◽

pp. 427-435 ◽

Cited By ~ 26

Author(s):

Mysore V Tejesvi ◽

Basavanna Mahesh ◽

Monnanda S Nalini ◽

Harishchandra S Prakash ◽

Kukkundoor R Kini ◽

...

Keyword(s):

Endophytic Fungi ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Fungal Species ◽

Southern India ◽

Terminalia Arjuna ◽

Terrestrial Plants ◽

Large Reservoir ◽

Medicinal Tree ◽

Individual Trees

Endophytic fungi represent an interesting group of microorganisms associated with the healthy tissues of terrestrial plants. They represent a large reservoir of genetic diversity. Fungal endophytes were isolated from the inner bark segments of ethnopharmaceutically important medicinal tree species, namely Terminalia arjuna, Crataeva magna, Azadirachta indica, Holarrhena antidysenterica, Terminalia chebula, and Butea monosperma (11 individual trees), growing in different regions of southern India. Forty-eight fungal species were recovered from 2200 bark segments. Mitosporic fungi represented a major group (61%), with ascomycetes (21%) and sterile mycelia (18%) the next major groups. Species of Fusarium, Pestalotiopsis, Myrothecium, Trichoderma, Verticillium, and Chaetomium were frequently isolated. Exclusive fungal taxa were recovered from five of the six plant species considered for the study of endophytic fungi. Rarefaction indices for species richness indicated the highest expected number of species for bark segments were isolated from T. arjuna and A. indica (20 species each) and from C. magna (18 species).Key words: bark, endophytes, medicinal trees, southern India.

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Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

Plants ◽

10.3390/plants10040656 ◽

2021 ◽

Vol 10 (4) ◽

pp. 656

Author(s):

Evangelia Stavridou ◽

Georgios Lagiotis ◽

Parthena Kalaitzidou ◽

Ioannis Grigoriadis ◽

Irini Bosmali ◽

...

Keyword(s):

Ssr Markers ◽

Geographical Origin ◽

Expressed Sequence Tag ◽

Phenotypic Diversity ◽

Molecular Data ◽

Phenotypic Traits ◽

Dissimilarity Matrix ◽

Heterotic Groups ◽

Hrm Analysis ◽

Sesame Genotypes

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽

10.3390/d11120234 ◽

2019 ◽

Vol 11 (12) ◽

pp. 234 ◽

Cited By ~ 2

Author(s):

Eric A. Griffin ◽

Joshua G. Harrison ◽

Melissa K. McCormick ◽

Karin T. Burghardt ◽

John D. Parker

Keyword(s):

Phylogenetic Diversity ◽

Large Scale ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tree Diversity ◽

Trophic Levels ◽

Community Diversity ◽

And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

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A light and electron microscope study of the fungal endophytes in the sporophyte and gametophyte of Lycopodium cernuum with observations on the gametophyte–sporophyte junction

Canadian Journal of Botany ◽

10.1139/b92-008 ◽

1992 ◽

Vol 70 (1) ◽

pp. 58-72 ◽

Cited By ~ 40

Author(s):

Jeffrey G. Duckett ◽

Roberto Ligrone

Keyword(s):

Root Nodules ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Peninsular Malaysia ◽

Epidermal Cells ◽

Host Cells ◽

Wall Material ◽

Intercellular Spaces ◽

Host Cytoplasm ◽

Fungal Associations

The ventral epidermal cells of the photosynthetic, surface-living gametophytes of Lycopodium cernuum, collected from moist shaded banks in Peninsular Malaysia, contain an aseptate fungus. In some cells the hyphae are thick walled and form coils encapsulated by a thin layer of host wall material. In others the fungus is thin walled and shows limited differentiation into larger trunk hyphae and arbuscules. The adjacent host cytoplasm, separated from the fungus by a granular interfacial matrix, contains numerous chloroplasts, mitochondria, and microtubules. The hyphae contact the substratum via the ventral walls of the epidermal cells and the rhizoids are free from infection. In the protocorm and root nodules, aseptate hyphae initially colonize mucilage-filled schizogenous intercellular spaces. Subsequent invasion of the host cells is associated with the development of massive overgrowths of host wall material. The fungal associations in L. cernuum share a mixture of attributes otherwise found in different angiosperm mycorrhizae and in mycotrophic relationships in liverworts. Wall ingrowths are present in both the gametophyte and sporophyte cells in the placenta of L. cernuum. The very limited development of the placenta, compared with L. appressum, certain bryophytes and ferns, the diminutive size, and early senescence of the gametophytes of L. cernuum are all linked to the presence of the protocorm. This massive absorptive organ, homologous to a foot, in terms of its position in sporophyte ontogeny, but external to the parent gametophyte, derives its nutrition partly from photosynthesis and partly from its fungal endophyte. Key words: chloroplasts, Lycopodium, mycorrhiza, pteridophytes, root nodules, symbiosis, transfer cells.

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Two new species of Undifilum, fungal endophytes of Astragalus (locoweeds) in the United States

Botany ◽

10.1139/b2012-056 ◽

2012 ◽

Vol 90 (9) ◽

pp. 866-875 ◽

Cited By ~ 33

Author(s):

Deana L. Baucom ◽

Marie Romero ◽

Robert Belfon ◽

Rebecca Creamer

Keyword(s):

New Species ◽

New Mexico ◽

Random Amplified Polymorphic Dna ◽

Phylogenetic Analyses ◽

Fungal Endophytes ◽

Morphological Characteristics ◽

Its Region ◽

The United States ◽

Neighbor Joining

New species of Undifilum , from locoweeds Astragalus lentiginosus Vitman and Astragalus mollissimus Torr., are described using morphological characteristics and molecular phylogenetic analyses as Undifilum fulvum Baucom & Creamer sp. nov. and Undifilum cinereum Baucom & Creamer sp. nov. Fungi were isolated from dried plants of A. lentiginosus var. araneosus , diphysus , lentiginosus , and wahweapensis collected from Arizona, Oregon, and Utah, USA, and A. mollissimus var. biglovii , earleii , and mollissimus collected from New Mexico, Oklahoma, and Texas, USA. Endophytic fungi from Astragalus locoweeds were compared to Undifilum oxytropis isolates obtained from dried plant material of Oxytropis lamberteii from New Mexico and Oxytropis sericea from Arizona, Colorado, New Mexico, Utah, and Wyoming. Extremely slow growth in vitro was observed for all, and conidia, if present, were ellipsoid with transverse septa. However, in vitro color, growth on four different media, and conidium size differed between fungi from Astragalus spp. and U. oxytropis. Neighbor-joining analyses of internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GPD) gene sequences revealed that U. fulvum and U. cinereum formed a clade distinct from U. oxytropis. This was supported by neighbor-joining analyses of results generated from random amplified polymorphic DNA (RAPD) fragments using two different primers.

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Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Phytotaxa ◽

10.11646/phytotaxa.514.3.5 ◽

2021 ◽

Vol 514 (3) ◽

pp. 247-260

Author(s):

KASUN THAMBUGALA ◽

DINUSHANI DARANAGAMA ◽

SAGARIKA KANNANGARA ◽

THENUKA KODITUWAKKU

Keyword(s):

Sri Lanka ◽

Camellia Sinensis ◽

Endophytic Fungi ◽

Sequence Data ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tea Leaves ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Rdna Sequence Data

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

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