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RAxML tree based on ITS-nrLSU combined sequences of T. badium, T. depressum, T. verrucosivolvum and related species. Bootstrap (BS) values derived from Maximum Likelihood (ML) analysis (≥ 70%) and Posterior Probabilities (PPs) from Bayesian Inference (≥ 0.90) are shown above or beneath the branches at nodes. Novel sequences are printed in bold.
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Three excavated truffle species Tuber badium, T. depressum and T. verrucosivolvum were described and illustrated from southwest China. Molecular analyses based on ITS and ITS-nrLSU concatenated dataset revealed that these species are distinct from the known ones of Tuber. Tuber badium, T. depressum and T. verrucosivolvum differ from other species o...
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... Two members of the Geomoriaceae family, Geomorium australianum and Geomorium echinulatum, were included as outgroup. Taxa and clade names were managed and depicted in this work according to previous studies (Bonito et al. 2010b(Bonito et al. , 2013Alvarado et al. 2012a;Healy et al. 2016a;Kinoshita et al. 2016;Wan et al. 2016Wan et al. , 2017Guevara-Guerrero et al. 2018;Páez et al. 2018;Leonardi et al. 2019;Polemis et al. 2019). Information related to the sequences of included Tuber species, sister taxa and outgroup are available in Online Resource 1 Table S1. ...
... In our concatenated dataset used for the ASR analyses, out of the 3225 characters of the combined EF1α-ITS-LSU-RPB2 matrix, 1199 were parsimony informative. Based on the multilocus ML species tree, the topology of Tuber clades was largely congruent with previous studies (Fig. 3) (Bonito et al. 2010b(Bonito et al. , 2013Alvarado et al. 2012b;Healy et al. 2016a;Kinoshita et al. 2016;Wan et al. 2016Wan et al. , 2017Guevara-Guerrero et al. 2018;Páez et al. 2018;Leonardi et al. 2019;Polemis et al. 2019;Fan et al. 2022). The ML bootstrap values of the branches of all thirteen clades were over 90%. ...
... l T. lacunosum (Alvarado et al. 2012a). m T. depressum (Wan et al. 2017) spiny ornamentation occurs in species of the Melanosporum and Rufum clades, and emerges at the MRCA of these two clades. In the lineage formed by the Melanosporum and Rufum clades, the spiny ornamentation is retained in some species, while the spino-reticulate and smooth spores evolved nine times and once, respectively. ...
The genus Tuber comprises ectomycorrhizal fungal species producing belowground ascomata, including the gastronomically most prominent hypogeous fungi. Since the discovery and description of new species are ongoing, the proportion of undescribed species can be considerable and the taxonomy of the genus goes often through changes. The taxonomy of the genus Tuber would therefore benefit from a periodic review. Tuber species described in Europe in recent decades include Tuber regianum , T. bernardinii and T. magentipunctatum . The common characteristics of these three species are the relatively small-sized spores with alveolate-reticulate ornamentation, a high number of spores per ascus (most frequently 6–8 spores) and small-sized ascomata with a verrucose-papillate or smooth surface. The present study aimed at examining the morphology and ecology of the three species, and providing a detailed taxonomic description of the Regianum clade using a multilocus phylogenetic analysis. In addition to this, we examined whether the apparently plesiomorphic morphological character states of this phylogenetically basal clade are the result of the conservation of ancestral character states. Our results show that in the case of certain morphological traits of the Regianum clade, the apparently plesiomorphic character states are indeed retained ancestral states, while in others, they are convergently reappeared ones. Furthermore, taking an overlook at all Tuber clades, we found that some morphological characters, such as spore length, number of spores per ascus and ascus length, changed together in the same evolutionary patterns, while others transformed in different ways within the genus.
Three new species of Tuber, T. albicavum, T. laojunshanense, and T. umbilicicavatum belonging to the Puberulum phylogroup, are described based on specimens collected in alpine Abies forests at 3600–4000 m, Northwest Yunnan, China. T. albicavum is distinguished by its ascomata with a single chamber of 0.5–1.8 cm diameter, with an apical opening of 0.2–0.6 cm in diameter, and light golden-brown alveolate reticulate ascospores up to 30 μm in length; T. laojunshanense is characterized by having ascomata with a slightly tomentose surface, sometimes with a white navel, a relatively thick peridium, up to 280 µm, and yellow-brown spores with alveolate reticulate ornamentation, up to 34 µm in length; T. umbilicicavatum is characterized by smooth ascomata with a distinct white navel, a relatively thin peridium, up to 110 µm, and golden or golden-brown alveolate reticulate ascospores, up to 40 μm in length. The molecular analysis of the internal transcribed spacer region also supports that these three new species differ from previously described Tuber species.
The genus Tuber (Tuberaceae, Pezizales) is an important fungal group of Ascomycota both economically and ecologically. However, the species diversity, phylogenetic relationships, and geographic distribution of Tuber species in China remains poorly understood, primarily because descriptions of many new species relied heavily on morphological features with molecular data either not sought or ignored. The misapplication of European and North American names further added to confusion regarding the taxonomy of Chinese Tuber species. In this study, we examined more than 1 000 specimens from China, and performed a comprehensive phylogenetic analysis for Chinese Tuber species using ITS sequences and multilocus sequence data. To infer the phylogeny of Chinese Tuber spp., 11 molecular datasets were assembled, including a concatenated internal transcribed spacers of the nuc rDNA (ITS), nuc rDNA 28S subunit (LSU), translation elongation factor 1-alpha (tef1-α), and RNA polymerase II subunit (rpb2) dataset as well as 10 ITS datasets (totally including 1 435 sequences from 828 collections with 597 newly generated sequences, and 168 sequences from the types of 63 species). Our phylogenetic tree based on a concatenated multilocus dataset revealed that all Chinese Tuber species nested in nine phylogenetic clades (phylogroups), including Aestivum, Excavatum, Latisporum, Macrosporum, Maculatum, Melanosporum, Puberulum, Rufum and Turmericum. Of these, five phylogroups (Macrosporum, Maculatum, Melanosporum, Puberulum and Rufum) are shared across the continents of Asia, Europe and North America; two phylogroups (Aestivum and Excavatum) are shared by Europe and Asia; and the phylogroups Turmericum and Latisporum are endemic only to Asia. Phylogenetic trees based on 10 ITS datasets confirmed the presence of at least 82 phylogenetic species in China. Of these, 53 are identified as known species, including three new records for China, and 25 species are identified as new to science. Of the new species, nine are described and illustrated in this paper, and the others remain unnamed due to the paucity or absence of ascomatal materials. Accordingly, the confirmed, excluded and doubtful Tuber species in China are discussed. Tuber species showed high endemism. Of the 82 phylogenetic species found in China, 68 species occur only in China, six species are also found in other regions in Asia, and only eight species (T. anniae, T. excelsum-reticulatum, T. formosanum, T. maculatum, T. wenchuanense, Tuber sp. CHN-3, Tuber sp. CHN-10 and Tuber sp. CHN-11) are shared with other continents. Most Tuber species have a small and limited distribution in China, but a few, such as T. formosanum and T. parvomurphium, are widely distributed across China. Some phylogenetically closely related species, such as T. liaotongense and T. subglobosum, as well as T. xuanhuaense and T. lijiangense, show a pattern of allopatric distribution.
Perhaps with the exception of a small number of cultivated saprobic species, the true truffles (Tuber spp.) command the attention of more scientists than other species of mushroom. Many thousands of scientific papers have been devoted to topics ranging among taxonomy; aroma; molecular makeup; the food, pharmaceutical, and cosmetics industries; and perhaps, at the bottom of the list, their cultivation. The genus Tuber is widespread in the northern hemisphere and with the recent exploration of new areas and the application of molecular identification methods, the number of proposed species is growing almost exponentially. The past 25 years in particular have seen a huge expansion in the cultivation of Tuber melanosporum, T. borchii, and T. aestivum in the Southern Hemisphere and a flurry of papers dealing with various molecular aspects of the truffles. This has resulted in a greater understanding of how to grow truffles in areas which would have been considered totally unsuitable in the Northern Hemisphere, and a depth of knowledge that early 1970s/1980s’ researchers would never have conceived such as the cultivation of T. melanosporum on heavily limed, naturally very acidic soils. Our current review looks at the state of knowledge in the fields of biodiversity and ecology, biotechnological applications, and the cultivation of true truffles.
Truffles in the genus Tuber are hypogeus fungi that have a worldwide distribution. Despite this, knowledge about their diversity in the Middle East is very limited. In recent years, large quantities of truffles have been imported from Iran for being sold in Italy. While analyzing certain commercial batches of T. aestivum from Iran, we found some ascomata that resembled T. excavatum but had macro- and micromorphological features that were distinct from this species. They were subglobose, or depressed to slightly irregular, with a conspicuous basal cavity, grayish brown, brown, or pinkish gray, with a minutely papillose peridium. The gleba was pinkish gray in youth, brown at maturity, marbled with cream branched veins. Ascospores were broadly ellipsoid, with an irregular reticulum and distinctive long crests along the longitudinal axis, up to 9 µm high. Analysis of internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences showed that these specimens form a monphyletic and well-supported taxon within the Excavatum clade. Morphological and molecular analyses supported the proposal of the new species T. iranicum.
Recent collections of Tuber malacodermum from Spain, Corsica, and Mexico were compared in an integrative morphological and molecular phylogenetic framework, including study of type material. Phylogenetic analyses of nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) and nuc 28S rDNA (28S) regions showed that specimens from Spain and Corsica form a monophyletic group closely related to T. melosporum and T. rufum, whereas Mexican specimens form a clade within the T. lyonii species complex. Peridium and ascospore morphology contribute clear morphological distinctions among specimens from Spain and Corsica, Mexico, and the type specimen of T. malacodermum. Based on results of the morphological and molecular phylogenetic analyses, we assigned the specimens from Spain and Corsica to Tuber pustulatum, sp. nov., and the Mexican specimens to Tuber theleascum, sp. nov. We restrict T. malacodermum to the sole type material. Formal descriptions and illustrations of these taxa are provided. ARTICLE HISTORY
The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of “integrative taxonomy.” Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae
of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.
Edible ectomycorrhizal mushrooms (EEMMs) live in the soil in association with the roots of plants, other ectomycorrhizal fungi, and soil organisms, all of which compete for space and nutrients. Consequently, the success of introducing an edible ectomycorrhizal (EEM) fungus into soils with the intention of cultivation is entirely dependent on its ability to survive in this competitive environment. Studies on the composition and structure of ectomycorrhizal (EM) communities in both productive and nonproductive EEMM areas have contributed to a better understanding of the relationship that EEMMs establish with other EM fungi and the environment. These have included morphological studies, the use of molecular tools, and most recently metagenomic methodologies leading to new insights into soil EEMM ecology. In this chapter, we briefly describe the methods that have been used to study EM fungal communities and Web databases that can be used for the identification of ectomycorrhizas such as the recently released eMyCo. We also illustrate the studies that have been conducted on the EM communities in natural and cultivated ecosystems where the most important EEMMs are found.
