scholarly journals Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12625
Author(s):  
Yoonhee Cho ◽  
Ji Seon Kim ◽  
Yu-Cheng Dai ◽  
Yusufjon Gafforov ◽  
Young Woon Lim
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
White Rot Fungi ◽  
Morphological Differentiation ◽  
White Rot ◽  
Long Time ◽  
Sequence Databases ◽  
Species Descriptions ◽  
Taxonomic Evaluation

Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank.

scholarly journals Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section

PhytoKeys ◽  
2020 ◽  
Vol 159 ◽  
pp. 1-34
Author(s):  
Frida Eggens ◽  
Farzaneh Jafari ◽  
Mikael Thollesson ◽  
Simon Crameri ◽  
Shahin Zarre ◽  
...  
Keyword(s):  
Distribution Pattern ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Monophyletic Group ◽  
Limited Distribution ◽  
Previously Treated ◽  
Nuclear Loci ◽  
Species Descriptions

A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model.

Sequence Validation for the Identification of the White-Rot Fungi Bjerkandera in Public Sequence Databases

2014 ◽  
Vol 24 (10) ◽  
pp. 1301-1307 ◽  
Author(s):  
Paul Eunil Jung ◽  
Jonathan J. Fong ◽  
Myung Soo Park ◽  
Seung-Yoon Oh ◽  
Changmu Kim ◽  
...  
Keyword(s):  
White Rot Fungi ◽  
White Rot ◽  
Sequence Databases

Taxonomic assessment of Australian Eocyzicus species (Crustacea: Branchiopoda: Spinicaudata)

Zootaxa ◽  
2018 ◽  
Vol 4410 (3) ◽  
pp. 401 ◽  
Author(s):  
LISA TIPPELT ◽  
MARTIN SCHWENTNER
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Morphological Variability ◽  
Intraspecific Variability ◽  
Principal Component ◽  
Interspecific Variation ◽  
Canonical Variate ◽  
Molecular Phylogenetic ◽  
Morphological Species ◽  
Species Descriptions

Herein we describe nine species of Eocyzicus from Australia and re-describe the morphological variability of Eocyzicus parooensis Richter & Timms, 2005 and Eocyzicus argillaquus Timms & Richter, 2009. All species were previously delimited by molecular phylogenetic analyses and the species descriptions are based on the same individuals. Characters were scored with the aid of the taxonomic software DELTA. The morphological analyses largely corroborated the previously delimited species despite high levels of intraspecific variability that overlapped with interspecific variation in many instances. Morphological species delimitation was generally supported by principal component and canonical variate analyses. Characters best suited for morphological species identification were the numbers of growth lines on the carapace, the number of telsonic spines and the number of setae on the furca. 

OPTIMIZATION OF BIOMASS AND ENDO-B-1,4-GLUCANASE BY WHITE ROT FUNGI NATIVE FROM ARGENTINA

2017 ◽  
Vol 16 (11) ◽  
pp. 2581-2588
Author(s):  
Ernesto M. Giorgio ◽  
Maria I. Fonseca ◽  
Andrea L. Morales ◽  
Pedro D. Zapata ◽  
Laura L. Villalba
Keyword(s):  
White Rot Fungi ◽  
White Rot

The Onset of Lignin-Modifying Enzymes, Decrease of AOX and Color Removal by White-Rot Fungi Grown on Bleach Plant Effluents

1991 ◽  
Vol 24 (3-4) ◽  
pp. 189-198 ◽  
Author(s):  
V. P. Lankinen ◽  
M. M. Inkeröinen ◽  
J. Pellinen ◽  
A. I. Hatakka
Keyword(s):  
Lignin Peroxidase ◽  
Active Form ◽  
White Rot Fungi ◽  
Pulp Mill ◽  
Color Removal ◽  
Effluent Treatment ◽  
White Rot ◽  
White Rot Fungus ◽  
Lignin Peroxidases ◽  
Pulp Mill Effluents

Decrease of adsorbable organic chlorine (AOX) is becoming the most important criterion for the efficiency of pulp mill effluent treatment in the 1990s. Two methods, designated MYCOR and MYCOPOR which utilize the white-rot fungus Phanerochaete chrysosporium have earlier been developed for the color removal of pulp mill effluents, but the processes have also a capacity to decrease the amount of chlorinated organic compounds. Lignin peroxidases (ligninases) produced by P. chrvsosporium may dechlorinate chlorinated phenols. In this work possibilities to use selected white-rot fungi in the treatment of E1-stage bleach plant effluent were studied. Phlebia radiata. Phanerochaete chrvsosporium and Merulius (Phlebia) tremellosus were compared in shake flasks for their ability to produce laccase, lignin peroxidase(s) and manganese-dependent peroxidase(s) and to remove color from a medium containing effluent. Softwood bleaching effluents were treated by carrier-immobilized P. radiata in 2 1 bioreactors and a 10 1 BiostatR -fermentor. Dechlorination was followed using Cl ion and AOX determinations. All fungi removed the color of the effluent. In P. radiata cultivations AOX decrease was ca. 4 mg l−1 in one day. Apparent lignin peroxidase activities as determined by veratryl alcohol oxidation method were negligible or zero in a medium with AOX content of ca. 60 mg l−1, prepared using about 20 % (v/v) of softwood effluent. However, the purification of extracellular enzymes implied that large amounts of lignin peroxidases were present in the medium and, after the purification, in active form. Enzyme proteins were separated using anion exchange chromatography, and they were further characterized by electrophoresis (SDS-PAGE) to reveal the kind of enzymes that were present during AOX decrease and color removal. The most characteristic lignin peroxidase isoenzymes in effluent media were LiP2 and LiP3.

Revalorizing Lignocellulose for the Production of Natural Pharmaceuticals and Other High Value Bioproducts

2019 ◽  
Vol 26 (14) ◽  
pp. 2475-2484 ◽  
Author(s):  
Congqiang Zhang ◽  
Heng-Phon Too
Keyword(s):  
Clostridium Thermocellum ◽  
White Rot Fungi ◽  
Brown Rot ◽  
Cost Effective ◽  
White Rot ◽  
Chemical Pretreatment ◽  
Significant Challenge ◽  
Drug Molecules ◽  
Natural Medicine ◽  
Renewable Natural Resource

Lignocellulose is the most abundant renewable natural resource on earth and has been successfully used for the production of biofuels. A significant challenge is to develop cost-effective, environmentally friendly and efficient processes for the conversion of lignocellulose materials into suitable substrates for biotransformation. A number of approaches have been explored to convert lignocellulose into sugars, e.g. combining chemical pretreatment and enzymatic hydrolysis. In nature, there are organisms that can transform the complex lignocellulose efficiently, such as wood-degrading fungi (brown rot and white rot fungi), bacteria (e.g. Clostridium thermocellum), arthropods (e.g. termite) and certain animals (e.g. ruminant). Here, we highlight recent case studies of the natural degraders and the mechanisms involved, providing new utilities in biotechnology. The sugars produced from such biotransformations can be used in metabolic engineering and synthetic biology for the complete biosynthesis of natural medicine. The unique opportunities in using lignocellulose directly to produce natural drug molecules with either using mushroom and/or ‘industrial workhorse’ organisms (Escherichia coli and Saccharomyces cerevisiae) will be discussed.

Bacterial Community Coexisting with White-Rot Fungi in Decayed Wood in Nature

2021 ◽  
Author(s):  
Yosuke Iimura ◽  
Hisashi Abe ◽  
Yuichiro Otsuka ◽  
Yuya Sato ◽  
Hiroshi Habe
Keyword(s):  
Bacterial Community ◽  
White Rot Fungi ◽  
White Rot ◽  
Decayed Wood

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

scholarly journals Evaluation of Basidiomycetes Wild Strains Grown in Agro-Industrial Residues for Their Anti-Tyrosinase and Antioxidant Potential and for the Production of Biocatalysts

Fermentation ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 19
Author(s):  
Anastasia Zerva ◽  
Nikolaos Tsafantakis ◽  
Evangelos Topakas
Keyword(s):  
Biomass Conversion ◽  
White Rot Fungi ◽  
Ligninolytic Enzymes ◽  
Inhibitory Effect ◽  
Biologically Active ◽  
White Rot ◽  
Oxidative Enzymes ◽  
Industrial Residues ◽  
Pure Compounds ◽  
Wild Strains

White-rot basidiomycetes are the only microorganisms with the ability to produce both hydrolytic (cellulases and hemicellulases) and oxidative (ligninolytic) enzymes for degrading cellulose/hemicellulose and lignin. In addition, they produce biologically active natural products with important application in cosmetic formulations, either as pure compounds or as standardized extracts. In the present work, three wild strains of Basidiomycetes fungi (Pleurotus citrinopileatus, Abortiporus biennis and Ganoderma resinaceum) from Greek habitats were grown in agro-industrial residues (oil mill wastewater, and corn cob) and evaluated for their anti-tyrosinase and antioxidant activity and for the production of biotechnologically relevant enzymes. P. citrinopileatus showed the most interesting tyrosinase inhibitory activity, while A. biennis showed the highest DPPH(2,2-diphenyl-1-picryl-hydrazyl) scavenging potential. Corn cobs were the most appropriate carbon source for maximizing the inhibitory effect of fungal biomasses on both activities, while the use of oil mill wastewater selectively increased the anti-tyrosinase potential of P. citrinopileatus culture filtrate. All strains were found to be preferential lignin degraders, similarly to most white-rot fungi. Bioinformatic analyses were performed on the proteome of the strains P. citrinopileatus and A. biennis, focusing on CAZymes with biotechnological relevance, and the results were compared with the enzyme activities of culture supernatants. Overall, all three strains showed strong production of oxidative enzymes for biomass conversion applications.

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