scholarly journals Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids

2019 ◽  
Author(s):  
Sarah A. Unruh ◽  
J. Chris Pires ◽  
Lawrence Zettler ◽  
Luigi Erba ◽  
Igor Grigoriev ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Mycorrhizal Fungi ◽  
Phylogenetic Trees ◽  
Species Boundaries ◽  
Internal Transcribed Spacer Region ◽  
Orchid Species ◽  
The World ◽  
Orchid Mycorrhizal Fungi ◽  
Current Species ◽  
Tulasnella Calospora

ABSTRACTMost plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the genera Tulasnella, Ceratobasidium, and Serendipita are critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and to improve the taxonomic resources for these groups. We identified 32 fungal isolates with the internal transcribed spacer region and used shallow genome sequencing to functionally annotate these isolates. We constructed phylogenetic trees from 408 orthologous nuclear genes for 50 taxa representing 14 genera, 11 families, and five orders in Agaricomycotina. While confirming relationships among the orders Cantharellales, Sebacinales, and Auriculariales, our results suggest novel relationships between families in the Cantharellales. Consistent with previous studies, we found the genera Ceratobasidium and Thanatephorus of Cerabotasidiaceae to not be monophyletic. Within the monophyletic genus Tulasnella, we found strong phylogenetic signals that suggest a potentially new species and a revision of current species boundaries (e.g. Tulasnella calospora); however it is premature to make taxonomic revisions without further sampling and morphological descriptions. There is low resolution of Serendipita isolates collected. More sampling is needed from areas around the world before making evolutionary-informed changes in taxonomy. Our study adds value to an important living collection of fungi isolated from endangered orchid species, but also informs future investigations of the evolution of orchid mycorrhizal fungi.

scholarly journals Understanding the distribution of three species of epiphytic orchids in temperate Australian rainforest by investigation of their host and fungal associates

Lankesteriana ◽  
2015 ◽  
Vol 7 (1-2) ◽  
Author(s):  
Kelli Gowland ◽  
Ulrike Mathesius ◽  
Mark Clements ◽  
Adrienne Nicotra
Keyword(s):  
Mycorrhizal Fungi ◽  
Local Environment ◽  
Direct Consequence ◽  
Environmental Constraints ◽  
Terrestrial Orchid ◽  
Orchid Species ◽  
Epiphytic Orchids ◽  
Carbon Transfer ◽  
Orchid Mycorrhizal Fungi ◽  
Fungal Associates

Understanding the environmental constraints that affect species distributions are critical to the mainte- nance of biodiversity. The abundance of epiphytic organisms, those that grow on another substrate, such as a tree or rock, is a direct consequence of the avail- ability and distribution of these substrates (Ackerman et al. 1989). In the case of epiphytic orchids it is also due to the presence of orchid mycorrhizal fungi (OMF). For an orchid, crucial to its germination and establishment, is its association with an OMF. The OMF provides a carbon source to the developing orchid embryo (Rasmussen 1995). Although recipro- cal carbon transfer has been demonstrated in mature plants of a green, terrestrial, orchid species, Goodyera repens (Cameron et al. 2006), it is generally believed that OMF receive no immediate benefit from their association with orchids. Therefore, it would appear intuitive that orchids would associate with all OMF available within their local environment and that they would actively seek this association. 

scholarly journals A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols

2021 ◽  
Author(s):  
Juanjo Bermudez
Keyword(s):  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
The World ◽  
Comprehensive Comparison ◽  
High Level

SARS-Cov-2 genome sequencing has been identified as a fundamental tool for fighting the COVID-19 pandemic. It is used, for example, for identifying new variants of the virus and for elaborating phylogenetic trees that help to trace the spread of the virus. In the present study we provide a comprehensive comparison between the quality of the assemblies obtained from different sequencing protocols. We demonstrate how some protocols actively promoted by different high-level administrations are inefficient and how less-used alternative protocols show a significant increased performance. This increase of performance could lead to cheaper sequencing protocols and therefore to a more convenient escalation of the sequencing efforts around the world.

scholarly journals Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Muhammad Izuddin ◽  
Amrita Srivathsan ◽  
Ai Lan Lee ◽  
Tim Wing Yam ◽  
Edward L. Webb
Keyword(s):  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Urban Expansion ◽  
Urban Trees ◽  
Tree Bark ◽  
Orchid Species ◽  
Epiphytic Orchids ◽  
Biophysical Factors ◽  
Natural Establishment ◽  
Orchid Mycorrhizal Fungi

AbstractUrban expansion threatens biodiversity worldwide, therefore urban spaces need to be amenable to biodiversity conservation. On trees in urban environments, natural colonisation and successful translocation of epiphytic orchids are necessary to enhance urban biodiversity, and depend on the availability of compatible orchid mycorrhizal fungi (OMF). However, the extent of OMF presence and distribution, as well as niche requirements for the OMF, remain poorly studied. To identify and quantify OMF on urban trees as well as assess their suitability for native epiphytic orchids, we conducted high-throughput sequencing on tree bark and orchid root samples. OMF were detected at 60% of the study sites on 16% of 270 bark samples (from stem, fork, and branch microsites within each tree). OMF presence and richness on bark samples were related to multiple biophysical factors; in general, humus presence and precipitation levels were positively predictive of OMF presence and richness. We found Ceratobasidiaceae- and Serendipitaceae-associated OMF both on bark and within roots. Orchid species also showed differing mycorrhizal specificity. Sites associated with fungal genera Ceratobasidium, Rhizoctonia, and Serendipita were considered suitable habitats for seven orchid species. The results suggest that urban trees support OMF and are therefore suitable for native orchid species; however, OMF availability are largely constrained by biophysical factors. To maximise the likelihood of translocation success and consequent natural establishment, we propose that (micro)sites are screened for compatible OMF prior to any intervention.

Introduction, growth and persistence in situ of orchid mycorrhizal fungi

2007 ◽  
Vol 55 (6) ◽  
pp. 665 ◽  
Author(s):  
Penelope S. Hollick ◽  
Jen A. McComb ◽  
Kingsley W. Dixon
Keyword(s):  
Seed Germination ◽  
Mycorrhizal Fungi ◽  
Mycorrhizal Fungus ◽  
Growing Season ◽  
Summer Drought ◽  
Orchid Species ◽  
The Third ◽  
Orchid Mycorrhizal Fungi ◽  
Germination And Growth

The introduction, growth and persistence of orchid mycorrhizal fungi in situ were studied by using a seed-baiting method. A mycorrhizal fungus from the carousel spider orchid, Caladenia arenicola (Hopper & A.P.Br.), was introduced to sites within an area from which the orchid and fungus were absent, adjacent to a natural population of C. arenicola. In the first growing season, the fungus grew up to 50 cm from its introduction point, usually persisted over the summer drought into the second season and even into the third season, stimulating germination and growth to tuber formation of the seeds in the baits. Watering the inoculated areas significantly increased seed germination. This suggests that it is possible to reintroduce the mycorrhizal fungi either before or together with seeds of orchid species needing re-establishment in an area.

scholarly journals Interactions with mycorrhizal fungi in two closely related hybridizing orchid species

2014 ◽  
Vol 73 (1) ◽  
pp. 322-333 ◽  
Author(s):  
Alessia Luca ◽  
Francesca Bellusci ◽  
Giuseppe Pellegrino
Keyword(s):  
Polymerase Chain Reaction ◽  
Mycorrhizal Fungi ◽  
Parental Species ◽  
Reaction Products ◽  
Chain Reaction ◽  
Short Term ◽  
Orchid Species ◽  
Ecological Preferences ◽  
Orchid Mycorrhizal Fungi ◽  
Polymerase Chain

Abstract The nuclear ribosomal DNAwas used to identify the orchid mycorrhizal fungi found in roots of Orchis xbivonae and its parental species Orchis anthropophora and Orchis italica. Polymerase chain reaction products were sequenced and identified using the expanded database.We determined that closely related Tulasnellaceae are mycorrhizal in the three orchid taxa, suggesting that the mycorrhizal partner does not impair hybrid survival. This study demonstrates that O. xbivonae displays few differences in comparison with its two parental species in identity of its associated mycorrhizal fungi, it is a short- -term by-product of the hybridizing behavior of common pollinators, and thus it will not easily origin descendents with potential new genetic combinations and/or ecological preferences.

scholarly journals The Dark Side of Orchid Symbiosis: Can Tulasnella calospora Decompose Host Tissues?

2020 ◽  
Vol 21 (9) ◽  
pp. 3139 ◽  
Author(s):  
Martino Adamo ◽  
Matteo Chialva ◽  
Jacopo Calevo ◽  
Silvia De Rose ◽  
Mariangela Girlanda ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
Molecular Mechanisms ◽  
Plant Cell Wall ◽  
Dark Side ◽  
In Planta ◽  
Orchid Species ◽  
Degrading Enzymes ◽  
Wide Range ◽  
Genes Encoding ◽  
Tulasnella Calospora

Photosynthetic orchids associate with mycorrhizal fungi that can be mostly ascribed to the “rhizoctonia” species complex. Rhizoctonias’ phylogenetic diversity covers a variety of ecological/nutritional strategies that include, beside the symbiosis establishment with host plants, endophytic and pathogenic associations with non-orchid plants or saprotrophic soil colonization. In addition, orchid mycorrhizal fungi (OMF) that establish a symbiotic relationship with an orchid host can later proliferate in browning and rotting orchid tissues. Environmental triggers and molecular mechanisms governing the switch leading to either a saprotrophic or a mycorrhizal behavior in OMF remain unclear. As the sequenced OMF genomes feature a wide range of genes putatively involved in the degradation of plant cell wall (PCW) components, we tested if these transitions may be correlated with a change in the expression of some PCW degrading enzymes. Regulation of several genes encoding PCW degrading enzymes was evaluated during saprotrophic growth of the OMF Tulasnella calospora on different substrates and under successful and unsuccessful mycorrhizal symbioses. Fungal gene expression in planta was investigated in two orchid species, the terrestrial Mediterranean Serapias vomeracea and the epiphytic tropical Cattleya purpurata. Although we only tested a subset of the CAZyme genes identified in the T. calospora genome, and we cannot exclude therefore a role for different CAZyme families or members inside a family, the results showed that the degradative potential of T. calospora is finely regulated during saprotrophic growth and in symbiosis, often with a different regulation in the two orchid species. These data pose novel questions about the role of fungal PCW degrading enzymes in the development of unsuccessful and successful interactions.

scholarly journals Tulasnella calospora (UAMH 9824) retains its effectiveness at facilitating orchid symbiotic germination in vitro after two decades of subculturing

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Lawrence W. Zettler ◽  
Caleb J. Dvorak
Keyword(s):  
Mycorrhizal Fungi ◽  
Terrestrial Orchid ◽  
Orchid Species ◽  
The North ◽  
Symbiotic Germination ◽  
Germinating Seeds ◽  
Tulasnella Calospora

Abstract Background The technique of symbiotic germination—using mycorrhizal fungi to propagate orchids from seed in vitro—has been used as one method to cultivate orchids in North America and abroad for > 30 years. A long-held assumption is that mycorrhizal fungi used for this purpose lose their effectiveness at germinating seeds over time with repeated subculturing. Results We provide evidence for the lingering efficacy of one particular strain of Tulasnella calospora (266; UAMH 9824) to stimulate seed germination exemplified by the North American terrestrial orchid, Spiranthes cernua, as a case study. This fungus was originally acquired from roots from Spiranthes brevilabris in 1999 and sub-cultured during the two decades since. Seeds inoculated with the fungus in vitro developed to an advanced protocorm stage after 16 days, and leaf elongation was pronounced after 42 days. In a pilot study, seedlings co-cultured with Tulasnella calospora 266 were deflasked after 331 days and later transferred to soil under greenhouse conditions where they eventually initiated anthesis. During the course of two decades, seeds of 39 orchid species, cultivars and hybrids spanning 21 genera, germinated in vitro co-cultured with Tulasnella calospora 266. These orchids included temperate terrestrials and tropical epiphytes alike. Conclusions The sustained effectiveness of this fungus is noteworthy because it argues against the concept of mycorrhizal fungi losing their symbiotic capability through prolonged subculturing. This study serves as an example of why in situ habitat preservation is essential for the conservation of orchids as a source of potentially useful mycorrhizal fungi.

scholarly journals Tropical orchid mycorrhizae: potential applications in orchid conservation, commercialization, and beyond

Lankesteriana ◽  
2013 ◽  
Author(s):  
Joel Tupapac Otero ◽  
Ana Teresa Mosquera ◽  
Nicola S. Flanagan
Keyword(s):  
Mycorrhizal Fungi ◽  
Orchid Species ◽  
Orchid Conservation ◽  
Potential Applications ◽  
Pathogenic Interaction ◽  
Induce Resistance ◽  
Orchid Mycorrhizae ◽  
Orchid Mycorrhizal Fungi ◽  
Tropical Orchid ◽  
Plant Families

Orchid mycorrhizae are unique interactions in the plant kingdom involving all the orchids and a variety of fungi including Rhizoctonia. Orchids are one of the most charismatic plant families and include at least 20,000 species widely appreciated by specialist growers and scientists. They also include Vanilla, source of one of the most traded spices worldwide. Most mycorrhizal fungi belong to a group of basidiomycetes widely known for their pathogenic interaction with many crop plants including potatoes, rice, and beans. The main application of orchid mycorrhizal fungi is in the propagation of endangered and commercial orchid species, but we have recently documented an alternative use. The fungal symbionts of orchids have the ability to induce resistance to Rhizoctonia in rice plants, which opens new possibilities of biological control agents never previously imagined.

The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Second Generation ◽  
Emergency Situation ◽  
The World ◽  
Break Points ◽  
Sex With Men ◽  
Full Length Genome ◽  
Virus Strains ◽  
Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

scholarly journals Edible mycorrhizal fungi of the world: What is their role in forest sustainability, food security, biocultural conservation and climate change?

2021 ◽  
Author(s):  
Jesús Pérez‐Moreno ◽  
Alexis Guerin‐Laguette ◽  
Andrea C. Rinaldi ◽  
Fuqiang Yu ◽  
Annemieke Verbeken ◽  
...  
Keyword(s):  
Climate Change ◽  
Food Security ◽  
Mycorrhizal Fungi ◽  
Forest Sustainability ◽  
The World ◽  
Biocultural Conservation
Sign in / Sign up

Export Citation Format

Share Document