scholarly journals Applying a Modified Metabarcoding Approach for the Sequencing of Macrofungal Specimens from Fungarium Collections

2021 ◽  
Author(s):  
C. Gary Olds ◽  
Jessie W. Berta-Thompson ◽  
Justin J. Loucks ◽  
Richard A. Levy ◽  
Andrew W. Wilson
Keyword(s):  
Phylogenetic Analysis ◽  
Fungal Diversity ◽  
Sequence Data ◽  
Dna Barcode ◽  
Cost Effective ◽  
Effective Solution ◽  
Operational Taxonomic Units ◽  
Large Numbers ◽  
Fungal Dna ◽  
Sequence Quality

Premise: Fungaria are a largely untapped source for understanding fungal biodiversity. The effort and cost in producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor and cost-effective solution for sequencing the fungal DNA barcode from hundreds of specimens at once. Methods: A two-step PCR approach uses nested barcoded primers to nrITS2 sequence data. We applied this to 766 macrofungal specimens that represent a broad taxonomic sampling of the Dikarya, of which 382 Lactarius specimens are used to identify molecular operational taxonomic units (MOTUs) through a phylogenetic approach. Scripts in Python and R were used to organize sequence data and execute packages CutAdapt and DADA2 were used for primer removal and assessing sequence quality. Sequences were compared to NCBI and UNITE databases and Sanger-produced sequences. Results: Specimen taxonomic identities from nrITS2 sequence data are >90% accurate across all specimens sampled. Phylogenetic analysis of Lactarius sequences identified 20 MOTUs. Discussion: The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections in advancing fungal diversity identification and documentation.

scholarly journals New section and species in Talaromyces

MycoKeys ◽  
2020 ◽  
Vol 68 ◽  
pp. 75-113 ◽  
Author(s):  
Bing-Da Sun ◽  
Amanda J. Chen ◽  
Jos Houbraken ◽  
Jens C. Frisvad ◽  
Wen-Ping Wu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Relationship ◽  
Fungal Diversity ◽  
Agricultural Soil ◽  
Sequence Data ◽  
Morphological Characters ◽  
Complete Sequence ◽  
Soil Samples ◽  
The World

Talaromyces is a monophyletic genus containing seven sections. The number of species in Talaromyces grows rapidly due to reliable and complete sequence data contributed from all over the world. In this study agricultural soil samples from Fujiang, Guangdong, Jiangxi, Shandong, Tibet and Zhejiang provinces of China were collected and analyzed for fungal diversity. Based on a polyphasic approach including phylogenetic analysis of partial ITS, BenA, CaM and RPB2 gene sequences, macro- and micro-morphological analyses, six of them could not be assigned to any described species, and one cannot be assigned to any known sections. Morphological characters as well as their phylogenetic relationship with other Talaromyces species are presented for these putative new species. Penicillium resedanum is combined in Talaromyces section Subinflati as T. resedanus.

scholarly journals Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246575
Author(s):  
Brandon Landry ◽  
Jeannette Whitton ◽  
Anna L. Bazzicalupo ◽  
Oldriska Ceska ◽  
Mary L. Berbee
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Dna Barcode ◽  
Strong Support ◽  
Its Region ◽  
Morphological Identification ◽  
Appropriate Treatment ◽  
Fungal Dna ◽  
Close Relatives

Some but not all of the species of ’little brown mushrooms’ in the genus Galerina contain deadly amatoxins at concentrations equaling those in the death cap, Amanita phalloides. However, Galerina’s ~300 species are notoriously difficult to identify by morphology, and the identity of toxin-containing specimens has not been verified with DNA barcode sequencing. This left open the question of which Galerina species contain toxins and which do not. We selected specimens for toxin analysis using a preliminary phylogeny of the fungal DNA barcode region, the ribosomal internal transcribed spacer (ITS) region. Using liquid chromatography/mass spectrometry, we analyzed amatoxins from 70 samples of Galerina and close relatives, collected in western British Columbia, Canada. To put the presence of toxins into a phylogenetic context, we included the 70 samples in maximum likelihood analyses of 438 taxa, using ITS, RNA polymerase II second largest subunit gene (RPB2), and nuclear large subunit ribosomal RNA (LSU) gene sequences. We sequenced barcode DNA from types where possible to aid with applications of names. We detected amatoxins only in the 24 samples of the G. marginata s.l. complex in the Naucoriopsis clade. We delimited 56 putative Galerina species using Automatic Barcode Gap Detection software. Phylogenetic analysis showed moderate to strong support for Galerina infrageneric clades Naucoriopsis, Galerina, Tubariopsis, and Sideroides. Mycenopsis appeared paraphyletic and included Gymnopilus. Amatoxins were not detected in 46 samples from Galerina clades outside of Naucoriopsis or from outgroups. Our data show significant quantities of toxin in all mushrooms tested from the G. marginata s.l. complex. DNA barcoding revealed consistent accuracy in morphology-based identification of specimens to G. marginata s.l. complex. Prompt and careful morphological identification of ingested G. marginata s.l. has the potential to improve patient outcomes by leading to fast and appropriate treatment.

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae)

Phytotaxa ◽  
2013 ◽  
Vol 146 (1) ◽  
pp. 1 ◽  
Author(s):  
PETER B. HEENAN ◽  
ROB D. SMISSEN
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Papua New Guinea ◽  
New Genus ◽  
New Caledonia ◽  
Sequence Data ◽  
Morphological Characters ◽  
New Combinations ◽  
Southern South America ◽  
Dna Sequence Data

The generic taxonomy of the Nothofagaceae is revised. We present a new phylogenetic analysis of morphological characters and map these characters onto a recently published phylogenetic tree obtained from DNA sequence data. Results of these and previous analyses strongly support the monophyly of four clades of Nothofagaceae that are currently treated as subgenera of Nothofagus. The four clades of Nothofagaceae are robust and well-supported, with deep stem divergences, have evolutionary equivalence with other genera of Fagales, and can be circumscribed with morphological characters. We argue that these morphological and molecular differences are sufficient for the four clades of Nothofagaceae to be recognised at the primary rank of genus, and that this classification will be more informative and efficient than the currently circumscribed Nothofagus with four subgenera.        Nothofagus is recircumscribed to include five species from southern South America, Lophozonia and Trisyngyne are reinstated, and the new genus Fuscospora is described. Fuscospora and Lophozonia, with six and seven species respectively, occur in New Zealand, southern South America and Australia. Trisyngyne comprises 25 species from New Caledonia, Papua New Guinea and Indonesia. New combinations are provided where necessary in each of these genera.

An investigation of a cost-effective solution for multimedia medical information management

1995 ◽  
Vol 28 (6) ◽  
pp. 361-376 ◽  
Author(s):  
Ken Chee Keung Law ◽  
Horace Ho Shing Ip ◽  
Siu Lok Chan
Keyword(s):  
Information Management ◽  
Medical Information ◽  
Cost Effective ◽  
Effective Solution
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