contains both asexual and sexually reproducing species. This genus is divided in seven sections and currently has 105 accepted species. In this study we investigated the isolates that were obtained during a study of indoor air collected in Beijing, China. These indoor strains are resolved in four sections, seven of them are identified as,, and according to sequences, while 14 isolates have divergent sequences and are described here as nine new species. The new species are placed in four sections, namely sections,, and. They are described based on sequence data (ITS,, and ) in combination with phenotypic and extrolite characters. Morphological descriptions and notes for distinguishing similar species are provided for each new species. The recently described is synonymised with based on presented phylogenetic results.

We constructed nine sets of oligonucleotide primers on the basis of the results of DNA hybridization of cloned genes from Neurospora crassa and Aspergillus nidulans to the genomes of select filamentous ascomycetes and deuteromycetes (with filamentous ascomycete affiliations). Nine sets of primers were designed to amplify segments of DNA that span one or more introns in conserved genes. PCR DNA amplification with the nine primer sets with genomic DNA from ascomycetes, deuteromycetes, basidiomycetes, and plants revealed that five of the primer sets amplified a product only from DNA of the filamentous ascomycetes and deuteromycetes. The five primer sets were constructed from the N. crassa genes for histone 3, histone 4, beta-tubulin, and the plasma membrane ATPase. With these five primer sets, polymorphisms were observed in both the size of and restriction enzyme sites in the amplified products from the filamentous ascomycetes. The primer sets described here may provide useful tools for phylogenetic studies and genome analyses in filamentous ascomycetes and deuteromycetes (with ascomycete affiliations), as well as for the rapid differentiation of fungal species by PCR.

The is a relatively large order of with members frequently having positive and negative impact on human activities. Species within this order gain attention from various research fields such as food, indoor and medical mycology and biotechnology. In this article we give an overview of families and genera present in the and introduce an updated subgeneric, sectional and series classification for and. Finally, a comprehensive list of accepted species in the is given. The classification of the at family and genus level is traditionally based on phenotypic characters, and this classification has since been challenged using sequence-based approaches. Here, we re-evaluated the relationships between families and genera of the using a nine-gene sequence dataset. Based on this analysis, the new family is introduced and four known families are accepted:,, and. The includes 28 genera: 15 genera are accommodated in the (,,,,,,,,,,,,, and ), eight in the (,,,,,,, ), two in the (, ) and one in the (). The classification of the was not part of this study, but according to literature two genera are present in this family ( and ). The use of an infrageneric classification system has a long tradition in and. Most recent taxonomic studies focused on the sectional level, resulting in a well-established sectional classification in these genera. In contrast, a series classification in and is often outdated or lacking, but is still relevant,, the allocation of a species to a series can be highly predictive in what functional characters the species might have and might be useful when using a phenotype-based identification. The majority of the series in and are invalidly described and here we introduce a new series classification. Using a phylogenetic approach, often supported by phenotypic, physiologic and/or extrolite data, is subdivided in six subgenera, 27 sections (five new) and 75 series (73 new, one new combination), and in two subgenera, 32 sections (seven new) and 89 series (57 new, six new combinations). Correct identification of species belonging to the is difficult, but crucial, as the species name is the linking pin to information. Lists of accepted species are a helpful aid for researchers to obtain a correct identification using the current taxonomic schemes. In the most recent list from 2014, 339, 354 and 88 species were accepted. These numbers increased significantly, and the current list includes 446 (32 % increase), 483 (36 % increase) and 171 (94 % increase) species, showing the large diversity and high interest in these genera. We expanded this list with all genera and species belonging to the (except those belonging to ). The list includes 1 187 species, distributed over 27 genera, and contains MycoBank numbers, collection numbers of type and ex-type cultures, subgenus, section and series classification data, information on the mode of reproduction, and GenBank accession numbers of ITS, beta-tubulin (), calmodulin () and RNA polymerase II second largest subunit () gene sequences.© 2020 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V.

Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit. Thermoascus and Paecilomyces, both members of Thermoascaceae, also form ascospores lacking a furrow or slit, but are differentiated from Trichocomaceae by the production of asci from croziers and their thermotolerant or thermophilic nature. Phylogenetic analysis shows that Penicillium is polyphyletic. The genus is re-defined and a monophyletic genus for both anamorphs and teleomorphs is created (Penicillium sensu stricto). The genera Thysanophora, Eupenicillium, Chromocleista, Hemicarpenteles and Torulomyces belong in Penicilliums. str. and new combinations for the species belonging to these genera are proposed. Analysis of Penicillium below genus rank revealed the presence of 25 clades. A new classification system including both anamorph and teleomorph species is proposed and these 25 clades are treated here as sections. An overview of species belonging to each section is presented.New sections, all in Penicillium: sect. Sclerotiora Houbraken & Samson, sect. Charlesia Houbraken & Samson, sect. Thysanophora Houbraken & Samson,sect. Ochrosalmonea Houbraken & Samson, sect. Cinnamopurpurea Houbraken & Samson, Fracta Houbraken & Samson, sect. Stolkia Houbraken & Samson, sect. Gracilenta Houbraken & Samson, sect. Citrina Houbraken & Samson, sect. Turbata Houbraken & Samson, sect. Paradoxa Houbraken & Samson, sect. Canescentia Houbraken & Samson. New combinations:Penicillium asymmetricum (Subramanian & Sudha) Houbraken & Samson, P. bovifimosum (Tuthill & Frisvad) Houbraken & Samson, P. glaucoalbidum (Desmazières) Houbraken & Samson, P. laeve (K. Ando & Manoch) Houbraken & Samson, P. longisporum (Kendrick) Houbraken & Samson, P. malachiteum (Yaguchi & Udagawa) Houbraken & Samson, P. ovatum (K. Ando & Nawawi) Houbraken & Samson, P. parviverrucosum (K. Ando & Pitt) Houbraken & Samson, P. saturniforme (Wang & Zhuang) Houbraken & Samson, P. taiwanense (Matsushima) Houbraken & Samson. New names:Penicillium coniferophilum Houbraken & Samson, P. hennebertii Houbraken & Samson, P. melanostipe Houbraken & Samson, P. porphyreum Houbraken & Samson.

A sample of isolates from Talaromyces pinophilus (55 isolates) and closely related species (76 isolates) was sequenced at four loci, the data were analyzed using maximum likelihood analysis and the GCPSR. The isolates were subjected to growth studies on the recommended media for description of Talaromyces species. On the basis of the combined data, five new species were segregated out of T. pinophilus and placed in newly described species. The T. pinophilus species complex contains ten species. The three other new species, Talaromyces argentinensis, T. californicus and T. louisianensis were not a part of the T. pinophilus species complex but occurred in Talaromyces sect. Talaromyces. T. argentinensis produces a teleomorphic state and is phylogenetically and morphologically distinct from other Talaromyces species.Published by Elsevier Ltd.

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene. Talaromyces species and most species of Penicillium subgenus Biverticilliumsensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type strains and/or representative isolates of Talaromyces and related biverticillate anamorphic species. Extrolite profiles were compiled for all type strains and many supplementary cultures. All evidence supports our conclusions that Penicillium subgenus Biverticillium is distinct from other subgenera in Penicillium and should be taxonomically unified with the Talaromyces species that reside in the same clade. Following the concepts of nomenclatural priority and single name nomenclature, we transfer all accepted species of Penicillium subgenus Biverticillium to Talaromyces. A holomorphic generic diagnosis for the expanded concept of Talaromyces, including teleomorph and anamorph characters, is provided. A list of accepted Talaromyces names and newly combined Penicillium names is given. Species of biotechnological and medical importance, such as P. funiculosum and P. marneffei, are now combined in Talaromyces. Excluded species and taxa that need further taxonomic study are discussed. An appendix lists other generic names, usually considered synonyms of Penicillium sensu lato that were considered prior to our adoption of the name Talaromyces.Taxonomic novelties:New species - Talaromyces apiculatus Samson, Yilmaz & Frisvad, sp. nov. New combinationsand names - Talaromyces aculeatus (Raper & Fennell) Samson, Yilmaz, Frisvad & Seifert, T. albobiverticillius (H.-M. Hsieh, Y.-M. Ju & S.-Y. Hsieh) Samson, Yilmaz, Frisvad & Seifert, T. allahabadensis (B.S. Mehrotra & D. Kumar) Samson, Yilmaz & Frisvad, T. aurantiacus (J.H. Mill., Giddens & A.A. Foster) Samson, Yilmaz, & Frisvad, T. boninensis (Yaguchi & Udagawa) Samson, Yilmaz, & Frisvad, T. brunneus (Udagawa) Samson, Yilmaz & Frisvad, T. calidicanius (J.L. Chen) Samson, Yilmaz & Frisvad, T. cecidicola (Seifert, Hoekstra & Frisvad) Samson, Yilmaz, Frisvad & Seifert, T. coalescens (Quintan.) Samson, Yilmaz & Frisvad, T. dendriticus (Pitt) Samson, Yilmaz, Frisvad & Seifert, T. diversus (Raper & Fennell) Samson, Yilmaz & Frisvad, T. duclauxii (Delacr.) Samson, Yilmaz, Frisvad & Seifert, T. echinosporus (Nehira) Samson, Yilmaz & Frisvad, comb. nov. T. erythromellis (A.D. Hocking) Samson, Yilmaz, Frisvad & Seifert, T. funiculosus (Thom) Samson, Yilmaz, Frisvad & Seifert, T. islandicus (Sopp) Samson, Yilmaz, Frisvad & Seifert, T. loliensis (Pitt) Samson, Yilmaz & Frisvad, T. marneffei (Segretain, Capponi & Sureau) Samson, Yilmaz, Frisvad & Seifert, T. minioluteus (Dierckx) Samson, Yilmaz, Frisvad & Seifert, T. palmae (Samson, Stolk & Frisvad) Samson, Yilmaz, Frisvad & Seifert, T. panamensis (Samson, Stolk & Frisvad) Samson, Yilmaz, Frisvad & Seifert, T. paucisporus (Yaguchi, Someya & Udagawa) Samson & Houbraken T. phialosporus (Udagawa) Samson, Yilmaz & Frisvad, T. piceus (Raper & Fennell) Samson, Yilmaz, Frisvad & Seifert, T. pinophilus (Hedgcock) Samson, Yilmaz, Frisvad & Seifert, T. pittii (Quintan.) Samson, Yilmaz, Frisvad & Seifert, T. primulinus (Pitt) Samson, Yilmaz & Frisvad, T. proteolyticus (Kamyschko) Samson, Yilmaz & Frisvad, T. pseudostromaticus (Hodges, G.M. Warner, Rogerson) Samson, Yilmaz, Frisvad & Seifert, T. purpurogenus (Stoll) Samson, Yilmaz, Frisvad & Seifert, T. rademirici (Quintan.) Samson, Yilmaz & Frisvad, T. radicus (A.D. Hocking & Whitelaw) Samson, Yilmaz, Frisvad & Seifert, T. ramulosus (Visagie & K. Jacobs) Samson, Yilmaz, Frisvad & Seifert, T. rubicundus (J.H. Mill., Giddens & A.A. Foster) Samson, Yilmaz, Frisvad & Seifert, T. rugulosus (Thom) Samson, Yilmaz, Frisvad & Seifert, T. sabulosus (Pitt & A.D. Hocking) Samson, Yilmaz & Frisvad, T. siamensis (Manoch & C. Ramírez) Samson, Yilmaz & Frisvad, T. sublevisporus (Yaguchi & Udagawa) Samson, Yilmaz & Frisvad, T. variabilis (Sopp) Samson, Yilmaz, Frisvad & Seifert, T. varians (G. Sm.) Samson, Yilmaz & Frisvad, T. verruculosus (Peyronel) Samson, Yilmaz, Frisvad & Seifert, T. viridulus Samson, Yilmaz & Frisvad.

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.

As part of a worldwide survey of the indoor mycobiota, dust was collected from nine countries. Analyses of dust samples included the culture-dependent dilution-to-extinction method and the culture-independent 454-pyrosequencing. Of the 7 904 isolates, 2 717 isolates were identified as belonging to Aspergillus, Penicillium and Talaromyces. The aim of this study was to identify isolates to species level and describe the new species found. Secondly, we wanted to create a reliable reference sequence database to be used for next-generation sequencing projects. Isolates represented 59 Aspergillus species, including eight undescribed species, 49 Penicillium species of which seven were undescribed and 18 Talaromyces species including three described here as new. In total, 568 ITS barcodes were generated, and 391 beta-tubulin and 507 calmodulin sequences, which serve as alternative identification markers.

The genus Talaromyces was described by Benjamin in 1955 as a sexual state of Penicillium that produces soft walled ascomata covered with interwoven hyphae. Phylogenetic information revealed that Penicillium subgenus Biverticillium and Talaromyces form a monophyletic clade distinct from the other Penicillium subgenera. Subsequently, in combination with the recent adoption of the one fungus one name concept, Penicillium subgenus Biverticillium was transferred to Talaromyces. At the time, the new combinations were made based only on phylogenetic information. As such, the aim of this study was to provide a monograph on Talaromyces applying a polyphasic species concept, including morphological, molecular and physiological characters. Based on an ITS, BenA and RPB2 multigene phylogeny, we propose a new sectional classification for the genus, placing the 88 accepted species into seven sections, named sections Bacillispori, Helici, Islandici, Purpurei, Subinflati, Talaromyces and Trachyspermi. We provide morphological descriptions for each of these species, as well as notes on their identification using morphology and DNA sequences. For molecular identification, BenA is proposed as a secondary molecular marker to the accepted ITS barcode for fungi.