New Approach to an Old Problem: Incorporating Signal from Gap-Rich Regions of ITS and rDNA Large Subunit into Phylogenetic Analyses to Resolve the Peltigera canina Species Complex

ABSTRACTAmong many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.

Download Full-text

Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark ( Alaudala rufescens ) — Sand Lark ( A. raytal ) species complex (Aves, Passeriformes) reveal cryptic diversity

Zoologica Scripta ◽

10.1111/zsc.12422 ◽

2020 ◽

Vol 49 (4) ◽

pp. 427-439 ◽

Cited By ~ 2

Author(s):

Fatemeh Ghorbani ◽

Mansour Aliabadian ◽

Ruiying Zhang ◽

Martin Irestedt ◽

Yan Hao ◽

...

Keyword(s):

Species Complex ◽

Phylogenetic Analyses ◽

Cryptic Diversity

Download Full-text

Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus

Australian Systematic Botany ◽

10.1071/sb12028 ◽

2012 ◽

Vol 25 (6) ◽

pp. 418 ◽

Cited By ~ 23

Author(s):

Roy E. Halling ◽

Mitchell Nuhn ◽

Todd Osmundson ◽

Nigel Fechner ◽

James M. Trappe ◽

...

Keyword(s):

New Genus ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Elongation Factor ◽

Sister Group ◽

Molecular Data ◽

Translation Elongation ◽

Spore Deposit ◽

Large Subunit Rdna ◽

Translation Elongation Factor 1Α

Harrya is described as a new genus of Boletaceae to accommodate Boletus chromapes, a pink-capped bolete with a finely scabrous stipe adorned with pink scabers, a chrome yellow base and a reddish-brown spore deposit. Phylogenetic analyses of large-subunit rDNA and translation elongation factor 1α confirmed Harrya as a unique generic lineage with two species, one of which is newly described (H. atriceps). Some Chinese taxa were recently placed in a separate genus, Zangia, supported by both morphology and molecular data. Multiple accessions from Queensland, Australia, support the synonymy of at least three species in a separate Australian clade in the new genus, Australopilus. The truffle-like Royoungia is also supported as a separate lineage in this clade of boletes. Even though it lacks stipe characters, it possesses the deep, bright yellow to orange pigments in the peridium. Additional collections from Zambia and Thailand represent independent lineages of uncertain phylogenetic placement in the Chromapes complex, but sampling is insufficient for formal description of new species. Specimens from Java referable to Tylopilus pernanus appear to be a sister group of the Harrya lineage.

Download Full-text

A new species of Chlorociboria (Helotiales, Ascomycota) on herbaceous stems from China

Phytotaxa ◽

10.11646/phytotaxa.312.1.9 ◽

2017 ◽

Vol 312 (1) ◽

pp. 111

Author(s):

HUAN-DI ZHENG ◽

WEN-YING ZHUANG

Keyword(s):

New Species ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Central China ◽

Nuclear Ribosomal Dna ◽

Light Blue ◽

Ectal Excipulum ◽

A New Species

A new species, namely Chlorociboria herbicola, is discovered on herbaceous stems in central China. Morphologically, the new fungus is distinctive by the combination of light blue-green apothecia, rectangular cells in ectal excipulum, and elongate-ellipsoidal ascospores with rounded ends. Phylogenetic analyses of the internal transcribed spacer and large subunit of nuclear ribosomal DNA sequences confirm its ascription in Chlorociboria and distinction from the known species of the genus.

Download Full-text

Generic classification of some more hyphomycetes with solitary conidia borne on phialides

Canadian Journal of Botany ◽

10.1139/b98-104 ◽

1998 ◽

Vol 76 (9) ◽

pp. 1570-1583 ◽

Cited By ~ 7

Author(s):

W Gams ◽

K O'Donnell ◽

H -J Schroers ◽

M Christensen

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Elongation Factor ◽

28S Rdna ◽

New Combination ◽

Rdna Sequences ◽

28S Rdna Sequences ◽

Three New Species ◽

Morphological Species

Unlike most phialide-producing fungi that liberate a multiplicity of conidia from each conidiogenous cell, only single conidia are formed on phialide-like conidiogenous cells in Aphanocladium, Verticimonosporium, and some species of Sibirina. A group of isolates obtained from soil of native Artemisia tridentata (sagebrush) grassland in Wyoming and from desert soil in Iraq is compared with these genera and classified as a fourth genus, Stanjemonium, honouring Stanley J. Hughes. Phylogenetic analyses of partial nuclear small- (18S) and large-subunit (28S) rDNA sequences indicate that Stanjemonium spp. form a monophyletic group with Emericellopsis. Sequences from the nuclear 18S and 28S rDNA were too conserved to resolve morphological species of Stanjemonium; however, phylogenetic analysis of b-tubulin and translation elongation factor 1a gene exons and introns resolved all species distinguished morphologically. Numerous conidiogenous cells or denticles are scattered along the cells of aerial hyphae in Aphanocladium and Stanjemonium spp., very rapidly collapsing into denticles in the former, somewhat more persistent and leaving broad scars in the latter. In Cladobotryum-Sibirina and Verticimonosporium spp., conidiogenous cells are discrete in terminal and intercalary whorls; phialides of the latter taxon are particularly swollen. The taxonomy of Aphanocladium is not yet resolved. Two species are recognized in Verticimonosporium. Three new species of Stanjemonium are described, and one new combination from Aphanocladium is proposed, along with one new species of Cladobotryum.Key words: Aphanocladium, Cladobotryum, conidiogenesis, hyphomycetes, molecular phylogeny, phialide, Stanjemonium, systematics, Verticimonosporium.

Download Full-text

New Species of Tomentella (Thelephorales, Basidiomycota) from Temperate Continental Mountain Climate of China (Xinjiang Region)

Forests ◽

10.3390/f12111531 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1531

Author(s):

Xu Lu ◽

Haisheng Yuan

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Morphological Characteristics ◽

Northwest China ◽

Tropical Regions ◽

Mountain Climate ◽

Molecular Phylogenetic ◽

Three New Species ◽

Xinjiang Autonomous Region

Species in the genus Tomentella are distributed throughout the temperate and tropical regions worldwide, but few studies associated with the taxonomy and phylogeny of this genus had been reported from Northwest China. In this paper, molecular phylogenetic analyses of the nuclear ribosomal ITS (internal transcribed spacer: ITS1-5.8S-ITS2) and LSU (large subunit: 28S) sequences combined with morphological characteristics identified three new species from Xinjiang Autonomous Region in Northwest China, which were named T. aurantispora, T. kanasensis, and T. schrenkiana. Similar macromorphological and anatomical characteristics are shared by these new species: arachnoid basidiocarps; byssoid sterile margins; utriform basidia with a clamp connection at the base; the absence of rhizomorphs and cystidia; and slightly thick-walled, subglobose to globose basidiospores. Among these new species, the color of the hymenophoral surface, the size of the basidiospores, and some other features can be used for species delimitation. The new species and closely related species in the phylogenetic tree were discussed, and a key to the identified species of Tomentella from China was provided.

Download Full-text

Phylogeny and Synonymy of Gyrodinium heterostriatum comb. nov. (Dinophyceae), a Common Unarmored Dinoflagellate in the World Oceans [plus supplementary materials]

Acta Protozoologica ◽

10.4467/16890027ap.20.007.12675 ◽

2020 ◽

Vol 59 (2) ◽

pp. 77-87

Author(s):

Fernando Gómez ◽

Luis F. Artigas ◽

Rebecca J. Gast

Keyword(s):

North Sea ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Morphological Plasticity ◽

Sister Group ◽

Rrna Gene ◽

Microbial World ◽

The North ◽

The North Sea ◽

Environmental Sequences

The North Sea and the English Channel are regions with a long tradition of plankton studies, where the colony-forming haptophyte Phaeocystis globosa dominates the spring phytoplankton blooms. Among its predators, we investigated an abundant unarmored dinoflagellate (~3000 cells per liter) in the North Sea in May 2019. It has been reported in the literature as Gymnodinium heterostriatum or G. striatissimum, and often identified as Gyrodinium spirale. Phylogenetic analyses using the small-, large subunit- and Internal Transcriber Spacers of the ribosomal RNA (SSU-, LSU-, ITS rRNA) gene sequences indicate that our isolates clustered within the Gyrodinium clade. The new sequences formed a sister group with sequences of the freshwater taxon Gyrodinium helveticum, being one of the infrequent marine-freshwater transitions in the microbial world. This isolate is the first characterized member of a clade of numerous environmental sequences widely distributed from cold to tropical seas. This common and abundant taxon has received several names due to its morphological plasticity (changes of size and shape, often deformed after engulfing prey) and the difficulty in discerning surface striation. We conclude that the priority is for the species name Gymnodinium heterostriatum Kofoid & Swezy 1921, a new name that was proposed for Gymnodinium spirale var. obtusum sensu Dogiel 1906. The species Gyrodinium striatissimum (Hulburt 1957) Gert Hansen & Moestrup 2000 and Gymnodinium lucidum D. Ballantine in Parke & Dixon 1964 (=G. hyalinum M. Lebour 1925) are posterior synonyms. We propose Gyrodinium heterostriatum comb. nov. for Gymnodinium heterostriatum.

Download Full-text

Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

10.21203/rs.3.rs-289731/v1 ◽

2021 ◽

Author(s):

Blessing Amaka Ezeonuegbu ◽

Dauda Abdullahi Machido ◽

Clement Z. Whong ◽

Wisdom S. Japhet ◽

Clement Ameh Yaro ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Industrial Effluent ◽

Pcr Amplification ◽

Morphological Characterization ◽

Likelihood Method ◽

Internal Transcribed Spacer Region ◽

Fungal Isolates ◽

Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

Download Full-text

Morphological and molecular identification of a new species of Atraporiella (Polyporales, Basidiomycota) in China

Phytotaxa ◽

10.11646/phytotaxa.332.1.3 ◽

2017 ◽

Vol 332 (1) ◽

pp. 31 ◽

Cited By ~ 1

Author(s):

ZI-QIANG WU ◽

SHAN SHEN ◽

KAI-YUE LUO ◽

ZHENG-HUI WANG ◽

CHANG-LIN ZHAO

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Strong Support ◽

Molecular Data ◽

Fungal Species ◽

Monophyletic Lineage ◽

Inference Methods ◽

A New Species ◽

Molecular Characters

A new poroid wood-inhabiting fungal species, Atraporiella yunnanensis sp. nov., is proposed based on morphological and molecular characters. The species is characterized by cream pore surface when dry, which is easy to separate from substrate and very rapidly stained dark brown to black when bruised; hyphal system monomitic with generative hyphae hyaline to pale brown, thin-walled, unbranched, interwoven; slightly allantoid basidiospores, 2.2–3 × 0.8–1.5 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on molecular data of ITS+nLSU sequences showed that Atraporiella yunnanensis belonged to the residual polyporoid clade, formed a monophyletic lineage with a strong support (100% BS, 100% BP, 1.00 BPP) and was closely related to A. neotropica, and then grouped with other related genera: Antrodiella, Pouzaroporia, Steccherinum and Xanthoporus. Both morphological and molecular characters confirmed the placement of the new species in Atraporiella.

Download Full-text