Amplification and Direct Sequencing of Fungal Ribosomal Rna Genes for Phylogenetics

White, Thomas J.

doi:10.1016/b978-0-12-372180-8.50042-1

Cited by 25,740 publications

(20,555 citation statements)

References 15 publications

(12 reference statements)

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“…The internal transcribed spacer (ITS) region of rDNA was amplified using primer pairs ITS4 and ITS1F (White et al 1990). Amplification was performed in a 50 µL reaction volume which contained polymerase chain reaction (PCR) buffer (20 mM KCl, 10 mM (NH 4 ) 2 SO 4 , 2 mM MgCl 2 , 20 mM Tris-HCl, pH 8.4), 200 µm of each deoxyribonucleotide triphosphate, 15 pmols of each primer, c .…”

Section: Methodsmentioning

confidence: 99%

Community structure of endophytic fungi of four mangrove species in Southern China

Sun

Chen

et al. 2016

Mycology

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Mangrove forests play an important role in subtropical and tropical coastal ecosystems. Endophytic fungi are widely distributed in various ecosystems and have great contribution to global biodiversity. In order to better understand the effects of mangrove species and tissue types on endophytic fungal community, we investigated cultivable endophytic fungi in leaves and twigs of four mangroves Aegiceras corniculatum, Avicennia marina, Bruguiera gymnorrhiza, and Kandelia candel in Guangxi, China. The four tree species had similar overall colonisation rates of endophytic fungi (24–33%). The colonisation rates of endophytic fungi were higher in twigs (30–58%) than in leaves (6–25%) in the four plant species. A total of 36 endophytic fungal taxa were identified based on morphological characteristics and molecular data, including 35 Ascomycota and 1 Basidiomycota, dominated by Phomopsis, Phyllosticta, Xylaria, Leptosphaerulina, and Pestalotiopsis. The diversity of endophytic fungi was higher in twigs than in leaves in the four plant species. Some endophytic fungi showed host and tissue preference. The endophytic fungal community composition was different among four mangrove species and between leaf and twig tissues.

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Section: Methodsmentioning

confidence: 99%

Community structure of endophytic fungi of four mangrove species in Southern China

Sun

Chen

et al. 2016

Mycology

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“…DNA was extracted using a Qiagen DNeasy mini kit, following the Qiagen protocol, producing 200 µl of DNA extract for each isolate. Polymerase chain reaction (PCR) was carried out on the DNA extracts using the nrITS primers ITS1 and ITS4 (White et al 1990). The PCR reaction contained 1 μl of DNA extract (ca.…”

Section: Methodsmentioning

confidence: 99%

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

et al. 2015

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Endophytes associated with crops have potential as beneficial inoculants in agriculture, but little is known about their genetic diversity and phylogenetic relationships. We carried out the first ever ecological and phylogenetic survey of the culturable fungal root endophytes of a wild barley species. Fungal root endophytes were isolated from 10 populations of wall barley (Hordeum murinum), and 112 taxa of fungi were identified based on internal transcribed spacer sequence similarity. We found representatives from 8 orders, 12 families and 18 genera. Within this group, only 34 isolates (30% of the total) could be confidently assigned to a species, and 23 of the isolates (21% of the total) had no significant match to anything deposited in GenBank (based on <85% sequence similarity). These results suggest a high proportion of novel fungi, with 28% not assigned to a known fungal order. This includes three endophytes that have been shown to significantly improve agronomic traits in cultivated barley. This study has, therefore, revealed a profound diversity of fungal root endophytes in a single wild relative of barley. Extrapolating from this, the study highlights the largely unknown, hugely diverse and potentially useful resource of crop wild relative endophytes.

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“…To amplify the internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal region (ITS-5.8S region) used for fungal barcoding, the primer pairs ITS1 or ITS1F and ITS4 (White et al 1990) were used. The procedure used for polymerase chain reaction (PCR) and sequencing was previously described by Hosoya et al (2010).…”

Section: Methodsmentioning

confidence: 99%

A check list of non-lichenised fungi occurring on Fagus crenata, a tree endemic to Japan

2017

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Non-lichenised fungi from Fagus crenata, an endemic and major temperate tree species, were enumerated based on three approaches: fungarium specimens at the National Museum of Nature and Science; isolates obtained mainly from leaves and roots, and their molecular identification by barcoding region; and literature. In total, 209, 49, and 232 taxa were recognised from the fungarium specimens, isolates, and literature, respectively. Only three taxa were commonly observed using all three approaches. Moreover, the results demonstrate the diversity of fungi occurring on a single host plant species, and provide the basis for comparisons between fungi from Fagus spp. in other regions of the world.

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Amplification and Direct Sequencing of Fungal Ribosomal Rna Genes for Phylogenetics

Cited by 25,740 publications

References 15 publications

Community structure of endophytic fungi of four mangrove species in Southern China

Community structure of endophytic fungi of four mangrove species in Southern China

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

A check list of non-lichenised fungi occurring on Fagus crenata, a tree endemic to Japan

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