Fig 3 - uploaded by Thomas Læssøe
Content may be subject to copyright.
Phylogenetic relationships of species in the /Calochroi clade (Cortinarius section Calochroi) based on Bayesian analyses of ITS, RPB1 and RPB2 data. Fifty percent majority rule consensus cladogram based on 10,000 trees sampled in two Bayesian runs. Bayesian posterior probabilities are indicated above branches. Clades and groups discussed in the text are indicated, as well as major non-anthraquinonoid lineages as "N.A.". Morphological and ecological characters ware mapped as present (Wlled circle) or absent (empty cirlce): (A) anthraquinonoid pigments-pigment type were mapped according to Brandrud (1998): ATR, atrovirin; FLA, Xavomannin; FDM, Xavomannin 6,6-dimethylether; FTM, Xavomannin 6,6,8-trimethylether; 4OH-FDM, 4OHXavomannin 6,6-dimethylether; PHL, phlegmacin; PME, phlegmacin-8-methylether. (B) a pink alkaline reaction with sodagnitin on pileus, (C) d.o. on the bulb, (D) d.o. on the context, (E) pileus with blue, (F) pileus with yellow, (G) pale/colorless pileus, (H) blue lamellae, (I) yellow lamellae, (J) pale/colorless lamellae, (K) association with frondose trees, (L) association with coniferous trees.
Source publication
Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different...
Similar publications
A new species of agaricomycetes, Clitopilus lampangensis , is described based on collections from northern Thailand. This species was distinguished from previously described Clitopilus species by its pale yellow to grayish yellow pileus with the presence of wider caulocystidia. Molecular phylogenetic analyses, based on the data of the internal tran...
Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II ( rpb2 ) and translat...
Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species...
Phylogenetic relationships of 54 European Phlegmacium species, including members of most of the sections of classical systematics, were studied, integrating macro-, micromorphological and chemical characters of the basidiomes, as well as molecular phylogenetic analysis of nuclear rDNA sequences. Microscopical structures of the basidiomes were studi...
Tiger's Milk mushroom has been used for medicinal purposes by local aborigines to treat asthma, breast cancer, cough, fever and food poisoning. Molecular phylogenetic analysis utilizing RNA polymerase II, second largest subunit (RPB2) gene, identified the wild Tiger's Milk mushrooms collected from the state of Pahang in Malaysia for this study as L...
Citations
... Earlier, Cortinarius was considered as the largest genus in the order Agaricales, with reportedly 2250 species distributed throughout the world (Zhao et al. 2017, He et al. 2019. The Cortinariusgenus has been thoroughly studied in Europe and North America, (Frøslev et al. 2005, Garnica et al. 2005, Frøslev et al. 2007, Teasdale et al. 2013, 2020, 2022Garnica et al. 2016, Soop et al. 2019, while only a few species have been reported from other regions, particularly Asia (Peintner et al. 2004). Despite recent advances in molecular techniques, the diversity of this genus from the South Asian region, particularly from the Indian subcontinent remains poorly understood. ...
... Several studies have found that ITS barcode to be significantly effective in distinguishingCortinarius species (Garnica et al. 2016, Brandrud et al. 2018. The detailed studies of type specimens based on ITS sequence data inCortinarius include subgenus Phlegmacium (Fr.) Trog (Frøslev et al. 2007 and Telamonia (Fr.) Trog (Liimatainen et al. 2020). Similarly, several relatively large phylogenetic studies on the genus Cortinarius were published that delimited the species into several distinct sections and clades (Garnica et al. 2005, 2016, Harrower et al. 2011, Peintner et al. 2004, Soop et al. 2019, Stensrud et al. 2014, Liimatainen et al. 2017). ...
Phlegmacium kausaricum is a new species in the genus Phlegmacium reported from the Kashmir Himalaya, India, based on distinct morphological characters and molecular phylogenetic analysis of nrITS sequences. The species is characterized by pileus that is glutinous, glabrous with brownish universal veil remnants scattered over the surface, with incurved and entire thick margin. Lamellae are pale yellow, moderately crowded, adnate with crenulate margins. Stipe clavate (pear-shaped), greyish and tapering towards the end. Basidiospores 8.7–10.3 × 5.5–6.4 µm, amygdaliform. The odor is strong, pleasant like a banana. Molecularly, the ITS sequences differ from other species by at least 11 substitutions and 9 indel positions.
... For some groups of EMF, the ITS region is insufficient for molecular identification of closely related species. Some notable examples include Cenococcum (Obase et al., 2016) and Cortinarius (Frøslev et al., 2007;Niskanen et al., 2009). Cenococcum geophilum Fr. s.l. is probably the most widespread EMF species complex in the world. ...
... Some morphologically distinct and well-established species may produce identical ITS sequences (e.g. C. atrovirens Kalchbr. and C. ionocholorus Brandrud;Frøslev et al., 2007). Even in cases when they are not identical, the ITS sequences of discrete Cortinarius species often share >97 per cent similarity. ...
... As the ITS sequences of EMF often contain homopolymer sequences, 454 pyrosequencing can inf late the reported taxonomic diversity (Kunin et al., 2010) and cannot be reliably used for fungal groups characterized by low interspecific ITS variation (e.g. Cortinarius; Frøslev et al., 2007). ...
Mycorrhiza is a mutualistic symbiosis between some plant species and a diverse group of soil fungi. Mycorrhizal symbiosis is categorized into discrete types based on the structural differences and the taxonomic position of involved plants and fungi. The main types of mycorrhiza include arbuscular, ericoid, orchid, monotropoid and ectomycorrhiza, the latter being the main focus of this review. Identifying ectomycorrhizal fungi (EMF) is crucial for understanding the ecology and preservation of rare and endangered plants, fungi and habitats. Thus, since the discovery of ectomycorrhiza, new identification methods have been constantly developed. This review tracks the history of EMF identification methods, presents their limitations and aims to discern the frontier of the field. The early methods were based on the morphology and anatomy of EMF, which allowed ectomycorrhizae formed by different EMF to be distinguished. Recognizing the EMF species that formed them, however, was difficult. The introduction of molecular methods that analysed taxon-specific DNA barcodes was a breakthrough in EMF identification, and the internal transcribed spacer gene was adopted as a routine fungal barcoding sequence. Identifying EMF from randomly sampled roots by morphology or polymerase chain reaction (PCR)-based methods results in rare EMF taxa being missed and underreported. This is addressed by bulk sampling combined with environmental DNA metabarcoding methods, which, in turn, yield a lower resolution of taxonomic identification. Most EMF identification methods incorporate PCR reactions, which are biased against some groups of EMF; developing PCR-free molecular methods would constitute a significant advancement. As the traditional concept of species is challenging for fungi, studying EMF functional rather than taxonomic diversity appears to be promising.
... The most species-rich and complex subgenus is Telamonia and is characterized morphologically by species producing dry basidiomata with brownish pilei (with the exception of some bluish-purple, orange-red or whitish species) and dry stipes (Niskanen et al. 2011). Most telamonioid species have been reported from Europe and North America and a few from other regions, especially from Asia (Peintner et al. 2004, Frøslev et al. 2005, Garnica et al. 2005, Frøslev et al. 2007, Teasdale et al. 2013, Garnica et al. 2016, Li et al. 2015, Luo & Bau 2021. ...
During recent fieldwork at Azad Jammu and Kashmir (Pakistan), many basidiomycetes of the genus Cortinarius were collected from mixed coniferous Himalayan temperate forests. Their morphological characterization and phylogenetic analyses based on ITS and LSU sequence data yielded a well-delimited, new species within C. subgenus Telamonia sect Disjungendi. It is characterized by producing small and dry basidiomata with blackish brown conico-convex pilei when young and uplifted at maturity, dark brown lamellae, a fibrillose stipe and small basidiospores (9.4 × 5.5 µm in average).
... Unfortunately, except for some species, morphological characteristics are often not sufficient to identify Agaricales specimens to the species level. Morphological characteristics can vary within species according to geographic conditions, surrounding environments, and developmental stages [8,9]. Vice versa, different species may have similar morphology if they are closely related or have undergone convergent evolution [10,11]. ...
Agaricales species form pileate-stipitate fruiting bodies and play important roles in maintaining the terrestrial ecosystem as decomposers, symbionts, and pathogens. Approximately 23,000 Agaricales species have been known worldwide, and 937 species have been recorded in the Republic of Korea. However, most of them were identified solely based on morphological characteristics that often led to misidentifications. The specimens collected from 2018 to 2020 in the Republic of Korea were identified based on phylogenetic analysis of the internal transcribed spacer (ITS) sequences. Their identities were confirmed by microscopic characteristics. As a result, 14 Agaricales species were discovered for the first time in the Republic of Korea. They belonged to nine genera: Agaricus, Calocybe, Cortinarius, Hygrocybe, Inocybe, Lepista, Leucoagaricus, Marasmius, and Psathyrella. Detailed macroscopic and microscopic descriptions were provided to help distinguish these species. The morphological and molecular data provided in this study will serve as reliable references for the identification of Agaricales species.
... Systematics in Cortinarius is still challenging, as basidiomata of many species show a remarkable variety of forms and colors (Garnica et al. 2005, Stensrud et al. 2014). In the last two decades, this issue has been partially overcome with the use of molecular phylogenies based on the nuclear ribosomal Internal Transcribed Spacer (ITS) region, which has proved to be an appropriate marker for species level delimitation in Cortinarius (e.g., Frøslev et al. 2007, Garnica et al. 2011. In fact, the suitability of ITS region has been indicated in many studies and this nuclear genomic region has been proposed as barcode region for this genus (Peintner et al. 2003, Ortega et al. 2008, Garnica et al. 2009, Garnica et al. 2011, Stefani et al. 2014, Garnica et al. 2016. ...
... has been recognized either as a subgenus (Hoiland 1983, Hoiland 1985, Ammirati 1988, Singer 1986 or as a separate genus, distinguished in part by its basidiomata with yellow, orange, red or olive tinges due to the presence of various anthraquinone pigments (Ammirati 1989, Arnold et al. 1987, Keller 1979, Keller 1982, Moser 1986b. Most dermocyboid species have been described from Europe and North America (Peintner et al. 2004, Frøslev et al. 2005, Garnica et al. 2005, Frøslev et al. 2007, Teasdale et al. 2013, Garnica et al. 2016, while only few have been reported from other regions, particularly from Asia. Dermocybe species prefer poor, acidic coniferous or Betula forests or they are indifferent of forest type (Høiland 1983, Peintner 2008 (Saba et al. 2017, Song et al. 2019, Naseer et al. 2020. ...
The new species Cortinarius himalayanus is described and illustrated based on specimens collected from the Himalayan moist temperate Abies pindrow forest of Pakistan. Macro-scopically, this taxon is characterized by umbonate to subumbonate pilei, whose cuticle is reddish brown in the center and pale yellow towards the margins, yellowish brown lamellae, and cylindrical to clavate stipes showing yellowish brown to brown longitudinal-fibrillose veil remnants. Microscopically , C. himalayanus has ellipsoid to amygdaliform and finely verrucose basidiospores with an average size of 7.8 × 5 µm and avQ = 1.5. The new taxon is placed in Cortinarius subgenus Dermocybe based on a molecular phylogenetic analysis using ITS sequence data.
... Many of the names described before the arrival of molecular methods are synonyms . The extensive studies of type specimens from selected groups of Cortinariaceae have revealed that the percentage of synonyms in the names mainly described from Europe and North America ranges from 7% to 72% (Frøslev et al. 2007;Liimatainen et al. 2014Liimatainen et al. , 2020Liimatainen et al. , 2022. ...
... In Cortinarius, the ITS regions have served well both for delimitation and DNA barcoding of species (Garnica et al. 2016). Only in a few cases morphologically accepted species have had identical ITS sequence data (Frøslev et al. 2007). The intraspecific variation of ITS regions is usually low, below 1%, and individuals with identical ITS sequences can be found from different continents (Liimatainen et al. 2014. ...
Fungi play vital roles in ecosystems as endophytes, pathogens and saprobes. The current estimate of fungal diversity is highly
uncertain, ranging from 1.5 to 12 million, but only around 150,000 species have been named and classified to date. Since
the introduction of DNA based methods for species identification, the number of newly described taxa has increased from
approximately 1000 to around 2000 yearly. This demonstrates the importance of DNA based methods to identify and distinguish species, especially cryptic species. Many novel species from recent studies have been found in historically understudied
regions and habitats, but these still represent only a small percentage of the estimated species. In this paper, we examine 16
genera from the top 40 most speciose genera as listed in Species Fungorum as case studies to examine the diversity of taxa in
each genus. The genera treated herein are Cercospora, Diaporthe, Meliola, Passalora, Phyllachora, Phyllosticta, Pseudocercospora, Ramularia (ascomycetes) and Cortinarius, Entoloma, Inocybe, Marasmius, Psathyrella, Puccinia, Russula, Uromyces
(basidiomycetes). We critically evaluate the number of species in these genera and correlate these numbers with the number
of entries in GenBank. We introduce 18 new species Apiospora multiloculata, Candolleomyces thailandensis, Cortinarius
acutoproximus, Cortinarius melleoalbus, Cortinarius pacificus, Cortinarius parvoacetosus, Diaporthe guizhouensis, Entoloma
pseudosubcorvinum, Inocybe meirensongia, Marasmius albulus, Marasmius obscuroaurantiacus, Meliola camporesii, Phyllachora siamensis, Phyllosticta doitungensis, Picipes yuxiensis, Pseudocercospora vignae, Puccinia maureanui and Russula
inornata. We also introduce a new record of Candolleomyces cladii-marisci and Inocybe iringolkavensis. We discuss the
genera Colletotrichum and Pleurotus that are speciose, but do not occur in the top 40. We hypothesize whether there might be
more species in these genera and discuss why these genera have some of the largest number of species.
... Forming ectomycorrhizal associations mainly with the trees of Fagaceae (Castanea, Castanopsis, Chrysolepis, Fagus, Notholithocarpus, Quercus) and Pinaceae (Abies, Larix, Picea, Pinus, Pseudotsuga, Tsuga), some species also with Betulaceae (Alnus, Corylus, Carpinus), Cistaceae (Cistus, Helianthemum) and Malvaceae (Tilia) (Garnica et al. 2011). Most species are rare and have narrow ecological preferences (Frøslev et al. 2007), and the majority are calcicolous or calciphilous. ...
... This group has been recognized as a separate, well-supported lineage since early molecular studies (Peintner et al. 2004;Garnica et al. 2005) and is also supported by morphological characteristics, and here were propose a name for it in generic level. For the most recent morpho-genetic study of the group see Frøslev et al. (2007) and Garnica et al. (2009). ...
... Notes: This is the most species-rich lineage within the genus Calonarius. Most species are characterized by a combination of lamellae with a purplish tint or completely purplish and lack of anthraquinonoid pigments (Frøslev et al. 2007). The basidiomata are medium-to large-sized, pileocarpic, agaricoid (phlegmacioid) and the pileipellis is simplex. ...
Family Cortinariaceae currently includes only one genus, Cortinarius, which is the largest Agaricales genus, with thousands of species worldwide. The species are important ectomycorrhizal fungi and form associations with many vascular plant genera from tropicals to arctic regions. Genus Cortinarius contains a lot of morphological variation, and its complexity has led many taxonomists to specialize in particular on infrageneric groups. The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level. Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups. We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species. In addition, a wider 5-locus analysis of 245 species, from the Northern and Southern Hemispheres, was also done. Based on our results, a classification of the family Cortinariaceae into ten genera—Cortinarius, Phlegmacium, Thaxterogaster, Calonarius, Aureonarius, Cystinarius, Volvanarius, Hygronarius, Mystinarius, and Austrocortinarius—is proposed. Seven genera, 10 subgenera, and four sections are described as new to science and five subgenera are introduced as new combinations in a new rank. In addition, 41 section names and 514 species names are combined in new genera and four lecto- and epitypes designated. The position of Stephanopus in suborder Agaricineae remains to be studied. Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes. It provides a cost-efficient way to produce -omics data in species-rich groups. The -omics data was produced from fungarium specimens up to 21 years old, demonstrating the value of museum specimens in the study of the fungal tree of life. This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.
... Most researchers have used molecular markers to support their species identification (Garnica & al. 2003(Garnica & al. , 2005(Garnica & al. , 2009Peintner & al. 2003;Frøslev & al. 2005Frøslev & al. , 2007Ortega & al. 2008;Stensrud & al. 2014;Stefani & al. 2014;Liimatainen & al. 2017;Sesli & Liimatainen 2018). Garnica & al. (2005) and Frøslev & al. (2007) showed that the rDNA ITS region is a particularly useful marker for species level identification for Cortinarius. ...
... Most researchers have used molecular markers to support their species identification (Garnica & al. 2003(Garnica & al. , 2005(Garnica & al. , 2009Peintner & al. 2003;Frøslev & al. 2005Frøslev & al. , 2007Ortega & al. 2008;Stensrud & al. 2014;Stefani & al. 2014;Liimatainen & al. 2017;Sesli & Liimatainen 2018). Garnica & al. (2005) and Frøslev & al. (2007) showed that the rDNA ITS region is a particularly useful marker for species level identification for Cortinarius. ...
... Phylogenies by Garnica & al. (2005) and Frøslev & al. (2007) place C. osmophorus in C. sect. Calochroi (of C. subg. ...
Three Cortinarius species, C. barbatus , C. osmophorus, and C . Saturninus, have been identified as new records for the Turkish mycota based on macro- and micromorphological characters, and their identifications were supported by molecular (rDNA ITS) phylogenetic data. The Turkish specimens are illustrated, and their diagnostic characters are compared with published descriptions of the same species and related taxa.
... DQ663364) by 24 substitutions and indels. With its marginate bulb, vividly-colored yellow to orange viscid pileus, coarsely-ornamented limoniform to amygdaliform spores, absence of hypoderm, and the vinaceous red KOH reaction of the pileus, bulb, and veil, C. caryae possesses morphological characters consistent with section Calochroi as defined by Frøslev et al. (2007). This newly described species used to be referred to as C. olearioides in Quebec but, as demonstrated previously (Landry et al. 2021), our phylogenetic analysis of ITS sequences from Calochroi species show that C. caryae and C. olearioides are sister species, the latter being absent from the North American continent (Fig. 2). ...
... Authors (Fig. 2). Morphologically, its marginate bulb, vividly-colored viscid pileus, coarsely-ornamented limoniform to amygdaliform spores, absence of hypoderm, and vivid-red KOH reaction of the pileus and context are consistent with section Calochroi as defined by Frøslev et al. (2007). Cortinarius viridicarneus shows two characters that, combined, make it unique among the North American Calochroi: its strong anise odor and its yellow-green context, at least in some parts. ...
... EU57047) by 15 substitutions and indels. With its marginate bulb, viscid pileus vividly colored in mature specimens, moderately to coarsely ornamented limoniform to amygdaliform spores, absence of hypoderm, and the reddish brown KOH reaction of the pileus and bulb rim, C. olivaceolamellatus possesses morphological characters consistent with section Calochroi as defined by Frøslev et al. (2007). Interestingly, the innately fibrillose pileus, considered by these authors to be an exceptional character for the section, is also observed in the subclade formed in our phylogeny by C. olivaceolamellatus, C. xanthochlorus, and Cortinarius sp. ...
In this 8th contribution to the Fungal Systematics and Evolution series published by Sydowia, the authors formally describe 11 species: Cortinarius caryae, C. flavolilacinus, C. lilaceolamellatus, C. malodorus, C. olivaceolamellatus, C. quercophilus, C. violaceoflavescens, C. viridicarneus, Entoloma meridionale (Agaricales), Hortiboletus rupicapreus (Boletales), and Paraglomus peruvianum (Paraglomerales). The following new country records are reported: Bolbitius callistus (Agaricales) from Russia and Hymenoscyphus equiseti (Helotiales) from Sweden. Hymenoscyphus equiseti is proposed as a new combination for Lanzia equiseti, based on ITS and LSU sequence data in combination with morphological study.
... Cortinarius is an important ectomycorrhizal genus in the Agaricales and is known to be the largest agaric genus worldwide (e.g., Garnica et al. 2016;Liimatainen et al. 2017Liimatainen et al. , 2020Varga et al. 2019). Species recognition based on morphology is difficult in Cortinarius lineages due to overlapping species characteristics and variation within species (e.g., Frøslev et al. 2007;Niskanen et al. 2009Niskanen et al. , 2013Niskanen et al. , 2016Liimatainen et al. 2014Liimatainen et al. , 2015. ...
... In general, these coloration patterns are found across many of the lineages. Several previous studies (e.g., Frøslev et al. 2007;Liimatainen et al. 2017;Clericuzio et al. 2017;Bellanger 2018;Bellanger et al. 2018) have already demonstrated that the presence/absence of blue/violet hues in basidiomata of Cortinarius groups is highly misleading to distinguish phylogenetically supported species. ...
Section Anomali is a species-rich group in North America belonging to Cortinarius , the most diverse genus in the Agaricales. This study is based on extensive morphological investigations and molecular methods using 191 nrDNA ITS sequence data and recovered 43 phylogenetic species from which 14 are described here as new to science. We sequenced ten type materials which belonged to eight species. The synonymy of C. caesiellus with C. albidipes and C. copakensis with C. albocyaneus is proposed here. The North American occurrence of four species ( C. albocyaneus , C. anomalus , C. caninus , and C. tabularis ), so far known only from Europe, was confirmed. Thirteen species were not formally described here due to lack of relevant information. An identification key to the known Anomali species in North America is provided.
