Publications by authors named "Wen-Ying Zhuang"

34 Publications

Heterologous expression of a single fungal HR-PKS leads to the formation of diverse 2-alkenyl-tetrahydropyrans in model fungi.

Org Biomol Chem 2021 Oct 6;19(38):8377-8383. Epub 2021 Oct 6.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

2-Alkenyl-tetrahydropyrans belong to a rare class of natural products that exhibit broad antifungal activities. Their structural instability and rareness in nature have restrained their discovery and drug development. In this study, the heterologous expression of a single highly reducing polyketide synthase (HR-PKS, App1) from in leads to the formation of seven 2-alkenyl-tetrahydropyran derivatives including one known compound virensol C (1) and six new compounds (2-7). However, introducing App1 into resulted in the identification of additional two 2-alkenyl-tetrahydropyrans lacking the hydroxyl or methoxyl group at the C-2 position (8 and 9). The structures of the isolated compounds were elucidated by extensive spectroscopic analysis using NMR and HR-ESI-MS.
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http://dx.doi.org/10.1039/d1ob01501jDOI Listing
October 2021

Comparative molecular evolution of chitinases in ascomycota with emphasis on mycoparasitism lifestyle.

Microb Genom 2021 Sep;7(9)

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.

Chitinases are involved in multiple aspects of fungal life cycle, such as cell wall remodelling, chitin degradation and mycoparasitism lifestyle. To improve our knowledge of the chitinase molecular evolution of Ascomycota, the gene family of 72 representatives of this phylum was identified and subjected to phylogenetic, evolution trajectory and selective pressure analyses. Phylogenetic analysis showed that the chitinase gene family size and enzyme types varied significantly, along with species evolution, especially for groups B and C. In addition, two new subgroups, C3 and C4, are recognized in group C chitinases. Random birth and death testing indicated that gene expansion and contraction occurred in most of the taxa, particularly for species in the order Hypocreales (class Sordariomycetes). From an enzyme function point of view, we speculate that group A chitinases are mainly involved in species growth and development, while the expansion of genes in group B chitinases is related to fungal mycoparasitic and entomopathogenic abilities, and, to a certain extent, the expansion of genes in group C chitinases seems to be correlated with the host range broadening of some plant-pathogenic fungi in Sordariomycetes. Further selection pressure testing revealed that chitinases and the related amino acid sites were under positive selection in the evolutionary history, especially at the nodes sharing common ancestors and the terminal branches of Hypocreales. These results give a reasonable explanation for the size and function differences of chitinase genes among ascomycetes, and provide a scientific basis for understanding the evolutionary trajectories of chitinases, particularly that towards a mycoparasitic lifestyle.
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http://dx.doi.org/10.1099/mgen.0.000646DOI Listing
September 2021

New Species of (Fungi) Isolated from Soil in Southwestern China.

Biology (Basel) 2021 Aug 4;10(8). Epub 2021 Aug 4.

School of Agriculture, Ludong University, Yantai 264025, China.

Southwestern China belongs among the global biodiversity hotspots and the Daba Mountains are recognized as one of the priority conservation areas. During the exploration of fungal biodiversity from soil samples collected from Mount Daba, two species of were discovered as new to science based on phylogenetic analyses and morphological comparisons. sp. nov. is a sister taxon of and in the section ; and sp. nov., affiliated to the section , is closely related to and . The new species differ from their sisters in DNA sequences, growth rates, and morphological characteristics. Descriptions and illustrations of them are provided in detail.
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http://dx.doi.org/10.3390/biology10080745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8389673PMC
August 2021

Ascomycetes from the Qilian Mountains, China - Hypocreales.

MycoKeys 2020 12;71:119-137. Epub 2020 Aug 12.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Chinese Academy of Sciences Beijing China.

To investigate fungi from the Qilian Mountains in Gansu Province, ascomycetous specimens were collected and hypocrealean fungi were examined. Eighteen species belonging to six genera in the families Hypocreaceae and Nectriaceae were identified, including 11 species of and in Hypocreaceae and seven species of , , , and in Nectriaceae. Among them, and are new to science. DNA sequence analyses of combined ACL1, ITS, RPB2, and TEF1 regions confirmed their taxonomic placements. Morphological distinctions between the new species and their close relatives are discussed. is reported for the first time in China.
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http://dx.doi.org/10.3897/mycokeys.71.55009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438379PMC
August 2020

A multigene phylogeny toward a new phylogenetic classification of .

IMA Fungus 2019 7;10. Epub 2019 Jun 7.

Department of Biostatistics, Yale University, 135 College St, New Haven, CT 06510 USA.

Fungi in the class are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: ord. nov., and and fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification.
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http://dx.doi.org/10.1186/s43008-019-0002-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325659PMC
June 2019

Carbon metabolic profiling of strains provides insight into potential ecological niches.

Mycologia 2020 Mar-Apr;112(2):213-223. Epub 2020 Feb 4.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Many species are cosmopolitan and widespread free-living fungi in various ecological environment, and many are economically important in the fields of agriculture and industry. However, carbon metabolism profiles of species have not been characterized in detail. In this study, Biolog FF MicroPlates were used to contrast carbon utilization and the differences among five species, each representing a unique phenotype. Their metabolic abilities varied greatly. Species producing cellulases and chitinases and with phosphate-solubilizing activities exhibited high efficiency of substrate utilization, whereas low efficiency was shown by saline-alkaline-tolerant species that metabolized simple carbon sources. Species producing cellulases at high levels may be specified to decompose and assimilate cellulose and hemicellulose in woody substrates, and those producing chitinases may have mycoparasitic roles. Species with plant growth-promoting traits are good at uptake of exudates from plant roots. Overall, metabolic models reflect nutritional adaptation of to diverse niches in nature.
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http://dx.doi.org/10.1080/00275514.2019.1698246DOI Listing
March 2021

A four-locus phylogeny of rib-stiped cupulate species of (Helvellaceae, Pezizales) with discovery of three new species.

MycoKeys 2019 31;60:45-67. Epub 2019 Oct 31.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Institute of Microbiology, Chinese Academy of Sciences Beijing China.

species are ascomycetous macrofungi with saddle-shaped or cupulate apothecia. They are distributed worldwide and play an important ecological role as ectomycorrhizal symbionts. A recent multi-locus phylogenetic study of the genus suggested that the cupulate group of was in need of comprehensive revision. In this study, all the specimens of cupulate sensu lato with ribbed stipes deposited in HMAS were examined morphologically and molecularly. A four-locus phylogeny was reconstructed using partial sequences of the heat shock protein 90, nuclear rDNA internal transcribed spacer region 2, nuclear large subunit ribosomal DNA and translation elongation factor 1-α genes. Three clades were revealed in sensu stricto. Twenty species were included in the analysis, of which 13 are distributed in China. Three new species, , and , are described and illustrated in detail. A neotype was designated for . is a new record for China, while should be excluded from Chinese mycota. Hsp90 and ITS2 are recommended as useful supplementary barcodes for species identifications of the genus.
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http://dx.doi.org/10.3897/mycokeys.60.38186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838221PMC
October 2019

Two New Species and a New Chinese Record of Hypocreaceae as Evidenced by Morphological and Molecular Data.

Mycobiology 2019 23;47(3):280-291. Epub 2019 Jul 23.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China.

To explore species diversity of Hypocreaceae, collections from Guangdong, Hubei, and Tibet of China were examined and two new species and a new Chinese record were discovered. Morphological characteristics and DNA sequence analyses of the ITS, LSU, EF-1α, and RPB2 regions support their placements in Hypocreaceae and the establishments of the new species. sp. nov. is characterized by occurrence on fruitbody of sp., concentric rings formed on MEA medium, verticillium-like conidiophores, subulate phialides, rod-shaped to narrowly ellipsoidal conidia, and absence of chlamydospores. sp. nov. is distinguished by effuse to confluent rudimentary stromata lacking of a well-developed flank and not changing color in KOH, subcylindrical asci containing eight ascospores that disarticulate into 16 dimorphic part-ascospores, verticillium-like conidiophores, subcylindrical phialides, and subellipsoidal to rod-shaped conidia. Morphological distinctions between the new species and their close relatives are discussed. is found for the first time from China.
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http://dx.doi.org/10.1080/12298093.2019.1641062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6758621PMC
July 2019

The genera and (Hypocreales, Nectriaceae) in China.

MycoKeys 2019 1;55:101-120. Epub 2019 Jul 1.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Institute of Microbiology, Chinese Academy of Sciences Beijing China.

Recent collections and herbarium specimens of and from different regions of China were examined. Using combined analyses of morphological and molecular data, 17 species are recognised including three species of and 14 species in . Amongst them, and are new to science. on mossy bark is characterised by superficial, yellow to orange, pyriform to subglobose perithecia with a warted surface; ellipsoidal to broadly ellipsoidal, striate, uniseptate ascospores; and allantoid to rod-shaped, aseptate microconidia. possesses bright red perithecia with a slightly roughened surface and a prominently dark papilla; ellipsoidal, smooth, uniseptate ascospores; and subcylindrical, slightly curved, multiseptate macroconidia. Morphological distinctions and sequence divergences between the new species and their close relatives are discussed. Name changes for the previously recorded species in China are noted.
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http://dx.doi.org/10.3897/mycokeys.55.34527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614169PMC
July 2019

Three new species of from China as revealed by morphological and molecular evidences.

MycoKeys 2019 1;55:87-99. Epub 2019 Jul 1.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Institute of Microbiology, Chinese Academy of Sciences Beijing China.

Three new species of are introduced based on morphological characters and DNA sequence analyses (maximum parsimony and neighbor-joining methods), viz. , , and . All of them lack mucilaginous caps at ascospore poles. is distinguished by cream to yellowish white apothecia and slightly curved ascospores. is characterized by yellow apothecia, elliptical-fusoid ascospores 19-22 × 7-8.8 μm, and J+ asci 130-150 × 14-16.5 μm. is distinguished by orange apothecia and fusoid ascospores 16.5-25.3 × 3.3-3.5 μm. Descriptions and illustrations of the new species as well as a key to the known species in the genus are provided.
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http://dx.doi.org/10.3897/mycokeys.55.33859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6614148PMC
July 2019

A three-locus phylogeny of Gyromitra (Discinaceae, Pezizales) and discovery of two cryptic species.

Mycologia 2019 Jan-Feb;111(1):69-77. Epub 2018 Dec 13.

a State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , People's Republic of China.

Gyromitra species are known as "false morels" and produce cerebriform or discoid ascocarps. The genus is widely distributed in the Northern Hemisphere, and some species are poisonous. Infrageneric phylogenies based on 28S nuc rDNA (28S) are available, but molecular analyses derived from other genes are lacking. In this study, Gyromitra specimens deposited in HMAS were reexamined. Phylogenies inferred from 28S, nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2 = ITS), and the translation elongation factor 1-α (TEF1) gene were obtained, and four clades were revealed among 13 species. Two new cryptic species of Gyromitra, G. pseudogigas, sp. nov. and G. tianshanensis, sp. nov., are described. Gyromitra pseudogigas has saddle-shaped apothecia similar to those of G. infula and is sister to G. gigas in the phylogeny. Gyromitra tianshanensis clusters with G. infula and G. xinjiangensis but differs in morphology and sequence data.
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http://dx.doi.org/10.1080/00275514.2018.1515456DOI Listing
May 2019

Two new species of (Hypocreales) from Asia as evidenced by morphology and multi-gene analyses.

MycoKeys 2018 6(42):7-19. Epub 2018 Nov 6.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China Institute of Microbiology, Chinese Academy of Sciences Beijing China.

Two new species of are introduced, based on materials collected from central China. is characterised by gregarious, red brownish to dark red, oval-subglobose to globose perithecia that are formed on a basal stroma; (4-7-)8-spored cylindrical asci; ellipsoidal or rarely broadly ellipsoidal, uniseptate, smooth or finely verruculose ascospores; clavate, aseptate microconidia and absence of macroconidia. is characterised by red to bright red, pyriform, subglobose to globose, perithecia on a basal stroma, collapsing laterally when dry; subcylindrical to clavate asci with a rounded apex; ellipsoidal, uniseptate ascospores; and falcate, multiseptate macroconidia with an arcuate tip. Morphological distinctions of the new species from the related fungi are discussed. This is the first report of from Asia.
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http://dx.doi.org/10.3897/mycokeys.42.27664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234223PMC
November 2018

The complete mitochondrial genome of the bambusicolous fungus (Nectriaceae, Ascomycota).

Mitochondrial DNA B Resour 2018 Oct 27;3(2):1147-1148. Epub 2018 Oct 27.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China.

The complete nucleotide sequence of the mitochondrial genome of the bambusicolous fungus was determined using the next-generation sequencing technology. The circular molecule is 63,593 bp long with a GC content of 31.92%. Gene prediction revealed 44 genes encoding 15 conserved proteins, 27 tRNAs, and the large and small ribosomal RNAs. All genes are located on the same strand. The tRNA genes contain codons for all 20 standard amino acids. It turns out to be similar to the previously sequenced mitochondrial genomes of and . The differences lie in the number of introns embodied in protein-coding genes. Four introns exist in the mitochondrial genome of , 10 in , and 14 in . The phylogenetic analysis confirmed as a member of (Nectriaceae). The mitochondrial genome of will contribute to the understanding of phylogeny and evolution of the genus and family.
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http://dx.doi.org/10.1080/23802359.2018.1522979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871986PMC
October 2018

Trichodermatides E and F from fungus .

J Asian Nat Prod Res 2019 Jul 23;21(7):659-665. Epub 2018 Apr 23.

a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China.

Two new polyketide derivatives, trichodermatides E () and F (), are unprecedented examples of a polyketide with 6/6/6/6 tetracyclic skeleton, together with five known analogs koninginin B (), koninginin D (), 7-O-methylkoninginin D (), koninginins E and F (-), were isolated from the plant endophytic fungus . The structures of these two compounds were determined by NMR data and HR-ESI-MS analysis. The putative biosynthesis of compounds - was presented.
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http://dx.doi.org/10.1080/10286020.2018.1465051DOI Listing
July 2019

Richard Paul Korf (1925-2016).

Mycologia 2017 May-Jun;109(3):529-534. Epub 2017 Jul 31.

f State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , No. 1 Bei-Chen-Xi Road, Chaoyang District, Beijing , 100101 , China.

"With poetry, the tune is in the words themselves-and once you begin to hear it, it will stay with you." Richard P. Korf, notes to his narration of John Brown's Body.
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http://dx.doi.org/10.1080/00275514.2017.1360126DOI Listing
May 2018

Discovery from a large-scaled survey of Trichoderma in soil of China.

Sci Rep 2017 08 22;7(1):9090. Epub 2017 Aug 22.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

The first large-scaled survey of soil-inhabiting Trichoderma is conducted in 23 provinces of China. Twenty-three new species belonging to the green-ascospored clades are discovered. Their phylogenetic positions are determined by sequence analyses of the combined partial sequences of translation elongation factor 1-alpha and the second largest RNA polymerase subunit encoding genes. Morphology and culture characteristics are observed, described and illustrated in detail. Distinctions between the new species and their close relatives are compared and discussed. They are named as: T. aggregatum, T. alpinum, T. bannaense, T. breve, T. brevicrassum, T. byssinum, T. chlamydosporicum, T. concentricum, T. ganodermatis, T. hainanense, T. hengshanicum, T. hirsutum, T. hunanense, T. ingratum, T. liberatum, T. linzhiense, T. longisporum, T. polypori, T. pseudodensum, T. simplex, T. solum, T. undatipile and T. zayuense.
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http://dx.doi.org/10.1038/s41598-017-07807-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567330PMC
August 2017

Phylogeny and morphological analyses of Penicillium section Sclerotiora (Fungi) lead to the discovery of five new species.

Sci Rep 2017 08 15;7(1):8233. Epub 2017 Aug 15.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

Phylogeny of Penicillium section Sclerotiora is still limitedly investigated. In this study, five new species of Penicillium are identified from the samples collected from different places of China, and named P. austrosinicum, P. choerospondiatis, P. exsudans, P. sanshaense and P. verrucisporum. The conidiophores of P. austrosinicum and P. exsudans are monoverticillate like most members of the section, while the rest species are biverticillate similar to the only two species P. herquei and P. malachiteum previously reported in the section Sclerotiora. The phylogenetic positions of the new taxa are determined based on the sequence data of ITS, BenA, CaM and RPB2 regions, which reveals that all the species with biverticillate condiophores form a well-supported subclade in the section. The new Penicillium species clearly differ from the existing species of the genus in culture characteristics on four standard growth media, microscopic features, and sequence data. Morphological discrepancies are discussed between the new species and their allies.
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http://dx.doi.org/10.1038/s41598-017-08697-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557846PMC
August 2017

Three New Soil-inhabiting Species of Trichoderma in the Stromaticum Clade with Test of Their Antagonism to Pathogens.

Curr Microbiol 2017 Sep 19;74(9):1049-1060. Epub 2017 Jun 19.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

Trichoderma is a dominant component of the soil mycoflora. During the field investigations of northern, central, and southwestern China, three new species in the Stromaticum clade were encountered from soil, and named as T. hebeiense, T. sichuanense, and T. verticillatum. Their phylogenetic positions were determined by analyses of the combined two genes: partial sequences of translation elongation factor 1-alpha and the second largest RNA polymerase subunit-encoding genes. Distinctions between the new species and their close relatives were discussed. Trichoderma hebeiense appeared as a separate terminal branch. The species is distinctive by its oblong conidia and aggregated pustules in culture. Trichoderma sichuanense features in concentric colony and produces numerous clean exudates on aerial mycelium in culture. Trichoderma verticillatum is characterized by its verticillium-like synanamorph and production of abundant chlamydospores. In vitro antagonism towards the new species was tested by dual culture technique.
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http://dx.doi.org/10.1007/s00284-017-1282-2DOI Listing
September 2017

The complete mitochondrial genome of the important mycoparasite (Hypocreales, Ascomycota).

Mitochondrial DNA B Resour 2017 Mar 30;2(1):180-181. Epub 2017 Mar 30.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China.

The complete nucleotide sequence of mitochondrial genome of the important mycoparasitic fungus was determined using the next-generation sequencing technology. The circular molecule is 40,921 bp long with a GC content of 27.90%. Gene prediction revealed 42 genes encoding 15 conserved proteins, 25 tRNAs, the large and small ribosomal RNAs. All genes are located on the same strand. It is found to be similar to the previously sequenced mitochondrial genomes of and . The differences lie in the copy number of and locations of and . The phylogenetic analysis confirmed as a sister taxon of in (Bionectriaceae). The mitochondrial genome of will contribute to the understanding of phylogeny and evolution of Hypocreales.
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http://dx.doi.org/10.1080/23802359.2017.1303344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800572PMC
March 2017

Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade.

Sci Rep 2016 06 1;6:27074. Epub 2016 Jun 1.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China.

More than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed.
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http://dx.doi.org/10.1038/srep27074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888246PMC
June 2016

The complete mitochondrial genome of the important phytopathogen Nectria cinnabarina (Hypocreales, Ascomycota).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 11 2;27(6):4670-4671. Epub 2016 Mar 2.

a State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , P.R. China.

The complete nucleotide sequence of the mitochondrial genome of the important phytopathogic fungus Nectria cinnabarina was determined using the next-generation sequencing technology. The circular molecule is 69 895 bp long with a GC content of 28.71%. Gene prediction revealed 42 genes encoding 15 conserved proteins, 25 tRNAs, the large and small ribosomal RNAs. All genes are located on the same strand. Compared with previously sequenced mitochondrial genomes of the other members of Nectriaceae, the composition and order of the protein and rRNA genes are highly conserved; however, the quantity and order of tRNA genes are different. The phylogenetic analysis confirmed N. cinnabarina as a basal lineage in Nectriaceae. The mitochondrial genome of N. cinnabarina will contribute to the understanding of phylogeny and evolution of Nectriaceae and Hypocreales.
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http://dx.doi.org/10.3109/19401736.2015.1106495DOI Listing
November 2016

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection.

IMA Fungus 2013 Jul 4;4(1):41-51. Epub 2013 Apr 4.

Systematic Mycology & Microbiology Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA;

With the recent changes concerning pleomorphic fungi in the new International Code of Nomenclature for algae, fungi, and plants (ICN), it is necessary to propose the acceptance or protection of sexual morph-typified or asexual morph-typified generic names that do not have priority, or to propose the rejection or suppression of competing names. In addition, sexual morph-typified generic names, where widely used, must be proposed for rejection or suppression in favour of asexual morph-typified names that have priority, or the latter must be proposed for conservation or protection. Some pragmatic criteria used for deciding the acceptance or rejection of generic names include: the number of name changes required when one generic name is used over another, the clarity of the generic concept, their relative frequencies of use in the scientific literature, and a vote of interested mycologists. Here, twelve widely used generic names in three families of Hypocreales are proposed for acceptance, either by conservation or protection, despite their lack of priority of publication, or because they are widely used asexual morph-typified names. Each pair of generic names is evaluated, with a recommendation as to the generic name to be used, and safeguarded, either through conservation or protection. Four generic names typified by a species with a sexual morph as type that are younger than competing generic names typified by a species with an asexual morph type, are proposed for use. Eight older generic names typified by species with an asexual morph as type are proposed for use over younger competing generic names typified by a species with a sexual morph as type. Within Bionectriaceae, Clonostachys is recommended over Bionectria; in Hypocreaceae, Hypomyces is recommended over Cladobotryum, Sphaerostilbella over Gliocladium, and Trichoderma over Hypocrea; and in Nectriaceae, Actinostilbe is recommended over Lanatonectria, Cylindrocladiella over Nectricladiella, Fusarium over Gibberella, Gliocephalotrichum over Leuconectria, Gliocladiopsis over Glionectria, Nalanthamala over Rubrinectria, Nectria over Tubercularia, and Neonectria over Cylindrocarpon.
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http://dx.doi.org/10.5598/imafungus.2013.04.01.05DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719205PMC
July 2013

What an rRNA secondary structure tells about phylogeny of fungi in Ascomycota with emphasis on evolution of major types of ascus.

PLoS One 2012 26;7(10):e47546. Epub 2012 Oct 26.

State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.

Background: RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists.

Methodology/principal Findings: We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes.

Conclusions: Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0047546PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482189PMC
April 2013

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.

PLoS One 2011 Apr 21;6(4):e19039. Epub 2011 Apr 21.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America.

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019039PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080880PMC
April 2011

Two new species of Acervus (Pezizales) with a key to species of the genus.

Mycologia 2011 Mar-Apr;103(2):400-6. Epub 2010 Sep 19.

Key Laboratory of Systematic Mycology and Lichenology, Chinese Academy of Sciences, Beijing 100101, China.

Studies on the genus Acervus from China are reviewed briefly. Six of the seven known species of the genus are currently recorded in this country. Acervus beijingense and A. changchunense are described as new based on morphological features and molecular data, and A. flavidus with minor emendation is added to the Chinese fungus flora. Phylogenetic relationships among four of the seven species of the genus are investigated based on the 28S rDNA sequence analysis. Species of the genus formed a single clade with high bootstrap support. The sequences of A. epispartius forma epispartius and that of A. flavidus obtained from materials in different geographical regions together formed a group with 100% bootstrap support. Ascospore size and shape are important criteria in the taxonomy of the genus and are phylogenetically informative. A dichotomous key to all described species of the genus is provided.
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http://dx.doi.org/10.3852/10-149DOI Listing
May 2011

Botrytis fabiopsis, a new species causing chocolate spot of broad bean in central China.

Mycologia 2010 Sep-Oct;102(5):1114-26

The State Key Laboratory of Agricultural Microbiology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei, China.

The current study was conducted to identify Botrytis spp. isolated from symptomatic broad bean plants grown in Hubei Province, China. Among 184 Botrytis strains, three distinct species, B. cinerea, B. fabae and a previously undescribed Botrytis sp., were identified based on morphology of colonies, sclerotia and conidia. The novel Botrytis sp. is described herein as a new species, Botrytis fabiopsis sp. nov. At 20 C B. fabiopsis grew on potato dextrose agar (PDA) at 12-13 mm d(-1), similar to B. fabae (13 mm d(-1)), but slower than B. cinerea (17-19 mm d(-1)). It formed pale gray colonies with short aerial mycelia and produced gray to black sclerotia in concentric rings on PDA. B. fabiopsis produced greater numbers of sclerotia than B. cinerea but fewer than B. fabae. Conidia produced by B. fabiopsis on broad bean leaves are hyaline to pale brown, elliptical to ovoid, wrinkled on the surface and are larger than conidia of B. fabae and B. cinerea. Phylogenetic analysis based on combined DNA sequence data of three nuclear genes (G3PDH, HSP60 and RPB2) showed that B. fabiopsis is closely related to B. galanthina, the causal agent of gray mold disease of Galanthus sp., but distantly related to B. fabae and B. cinerea. Sequence analysis of genes encoding necrosis and ethylene-inducing proteins (NEPs) indicated that B. fabiopsis is distinct from B. galanthina. Inoculation of broad bean leaves with conidia of B. fabiopsis caused typical chocolate spot symptoms with a similar disease severity to that caused by B. fabae but significantly greater than that caused by B. cinerea. This study suggests that B. fabiopsis is a new causal agent for chocolate spot of broad bean.
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http://dx.doi.org/10.3852/09-217DOI Listing
November 2010

Chaetopsinectria (Nectriaceae, Hypocreales), a new genus with Chaetopsina anamorphs.

Mycologia 2010 Jul-Aug;102(4):976-84

Key Laboratory of Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China.

Genus Chaetopsinectria is established to accommodate four species, previously assigned to Cosmospora, that possess Chaetopsina anamorphs, small and red perithecia not collapsing when dry, a typical Cosmospora perithecial wall structure, clavate asci, smooth or striate ascospores, sienna colonies on PDA, and on decaying debris or woody substrates. The segregation of the new genus from Cosmospora is well supported by sequence analyses of nuclear ribosomal DNA (ITS and 28S partial) with maximum parsimony and Bayesian methods. The molecular data indicate that the new genus is distantly related to Cosmospora coccinea Rabenh., the type species of Cosmospora sensu stricto, and its related fungi. Four new combinations, Chaetopsinectria chaetopsinae, C. chaetopsinae-catenulatae, C. chaetopsinae-penicillatae and C. chaetopsinae-polyblastiae, are proposed.
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http://dx.doi.org/10.3852/09-263DOI Listing
August 2010

Three new species of Neonectria (Nectriaceae, Hypocreales) with notes on their phylogenetic positions.

Mycologia 2010 Jan-Feb;102(1):142-52

Key Laboratory of Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China.

Collections of Bionectriaceae and Nectriaceae from Henan, Hubei and Guangdong provinces, China, were examined. Three new species, Neonectria confusa, N. shennongjiana and N. sinensis, are described and illustrated. Distinctions between the new species and their related taxa are discussed. Phylogenetic relationships among some Neonectria species are investigated based on analyses of nuclear ribosome DNA ITS1-5.8S-ITS2 and beta-tubulin partial sequences. Combined analyses of molecular and morphological data suggest that N. confusa and N. shennongjiana can be classified in Neonectria sensu stricto and N. sinensis in the N. mammoidea-Group. A key to the known species of Neonectria from China is provided.
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http://dx.doi.org/10.3852/08-224DOI Listing
April 2010
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