A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal: global meta-analysis of Tuber ITS rDNA

Department of Biology, Duke University, Durham, NC 27708-0338, USA.
Molecular Ecology (Impact Factor: 6.49). 10/2010; 19(22):4994-5008. DOI: 10.1111/j.1365-294X.2010.04855.x
Source: PubMed

ABSTRACT Truffles (Tuber) are ectomycorrhizal fungi characterized by hypogeous fruitbodies. Their biodiversity, host associations and geographical distributions are not well documented. ITS rDNA sequences of Tuber are commonly recovered from molecular surveys of fungal communities, but most remain insufficiently identified making it difficult to determine whether these sequences represent conspecific or novel taxa. In this meta-analysis, over 2000 insufficiently identified Tuber sequences from 76 independent studies were analysed within a phylogenetic framework. Species ranges, host associates, geographical distributions and intra- and interspecific ITS variability were assessed. Over 99% of the insufficiently identified Tuber sequences grouped within clades composed of species with little culinary value (Maculatum, Puberulum and Rufum). Sixty-four novel phylotypes were distinguished including 36 known only from ectomycorrhizae or soil. Most species of Tuber showed 1-3% intraspecific ITS variability and >4% interspecific ITS sequence variation. We found 123 distinct phylotypes based on 96% ITS sequence similarity and estimated that Tuber contains a minimum of 180 species. Based on this meta-analysis, species in Excavatum, Maculatum and Rufum clades exhibit preference for angiosperm hosts, whereas those in the Gibbosum clade are preferential towards gymnosperms. Sixteen Tuber species (>13% of the known diversity) have putatively been introduced to continents or islands outside their native range.

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Available from: Andrii Gryganskyi, Sep 26, 2015
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    • "Maximum likelihood bootstrap values are shown above branches. Sequences are labeled with Latin binomials, GenBank accession or collection number and geographical origin (Bonito et al., 2010). Table S1. "
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    ABSTRACT: In the Mediterranean region, patches of vegetation recovering from disturbance and transiently dominated by shrubs produce one of the world's most prized fungi, the black truffle (Tuber melanosporum). In these successional plant communities, we have fragmentary knowledge of the distribution of T. melanosporum in space among ectomycorrhizal (ECM) host species and in time. Molecular identification of hosts (RFLP) and fungi (ITS sequencing) and quantification of T. melanosporum mycelium (qPCR) were employed to evaluate the presence of T. melanosporum on four dominant ECM host species (Quercus ilex, Q. coccifera, Arbutus unedo, Cistus albidus) and the extent to which their respective ECM communities shared fungal diversity, over the course of development of truffle grounds, from recent unproductive brûlés to senescent ones where production has stopped. We found that truffle grounds host rich communities in which multi-host fungal species dominate in frequency. When considering both ECM tips and soil mycelia, we documented a dynamic and spatially heterogeneous pattern of T. melanosporum distribution in soils and a presence of ECM tips restricted to Q. ilex roots. This study advances our knowledge of the ecology of T. melanosporum, and provides insight into the extent of ECM fungal sharing among plant species that dominate Mediterranean landscapes. This article is protected by copyright. All rights reserved.
    Environmental Microbiology 12/2014; 17(8). DOI:10.1111/1462-2920.12741 · 6.20 Impact Factor
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    • "The term " truffle " is sometimes used to name all hypogeous mushrooms in general, but it specifically refers to the genus Tuber. Bonito et al. (2010) report at least 180 species of Tuber around the world, although only about 13 have commercial interest (Bonito et al., 2009). The quintessential truffles are the European black truffle (Tuber melanosporum Vittad.) and the Italian white truffle (Tuber magnatum Pico). "
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    ABSTRACT: Aim of study: In recent decades the cultivation of the black truffle Tuber melanosporum has expanded across all the Mediterranean-climate regions, but also to other regions outside the European standard for the species. We aim to describe the current extent of T. melanosporum cultivation. Area of study: Tuber melanosporum plantations in Europe, the Mediterranean basin, Australia, New Zealand, China, America and South Africa. Material and Methods: The socioeconomic impact of T. melanosporum cultivation, the way in which the current situation has been achieved and the knowledge needed for its progress are reviewed. Research highlights: T. melanosporum has been successfully cultivated in several countries outside its natural area, but many practices are still empirical and thus yields cannot be guaranteed. The recent advances in molecular techniques and genome science are helping to overcome some of the difficulties traditionally constraining truffle research. The role of truffles as a transitional element between agricultural and forestry activities makes its cultivation a paradigm of sustainable rural development.
    Forest Systems 07/2014; 23(2):317-328. DOI:10.5424/fs/2014232-04771 · 0.80 Impact Factor
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    • "The second identification criterion was based on the ITS sequences because some of the samples from Europe, North America and South Africa lacked rpb2, ef1-α and β-tubulin sequences in the GenBank database. In this method, the phylogenetic species were recognised according to the inter- and intra-specific variations of the ITS sequence, using criteria established to define phylogenetic or environmental species in previous studies [58-60]. Generally speaking, the intraspecific variations of some well-studied species were first compared, and then the highest variation was defined as the threshold to delimit species within this group. "
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    ABSTRACT: Background Lethal amanitas (Amanita section Phalloideae) are a group of wild, fatal mushrooms causing many poisoning cases worldwide. However, the diversity and evolutionary history of these lethal mushrooms remain poorly known due to the limited sampling and insufficient gene fragments employed for phylogenetic analyses. In this study, five gene loci (nrLSU, ITS, rpb2, ef1-α and β-tubulin) with a widely geographic sampling from East and South Asia, Europe, North and Central America, South Africa and Australia were analysed with maximum-likelihood, maximum-parsimony and Bayesian inference methods. Biochemical analyses were also conducted with intention to detect amatoxins and phalloidin in 14 representative samples. Result Lethal amanitas were robustly supported to be a monophyletic group after excluding five species that were provisionally defined as lethal amanitas based on morphological studies. In lethal amanitas, 28 phylogenetic species were recognised by integrating molecular phylogenetic analyses with morphological studies, and 14 of them represented putatively new species. The biochemical analyses indicated a single origin of cyclic peptide toxins (amatoxins and phalloidin) within Amanita and suggested that this kind of toxins seemed to be a synapomorphy of lethal amanitas. Molecular dating through BEAST and biogeographic analyses with LAGRANGE and RASP indicated that lethal amanitas most likely originated in the Palaeotropics with the present crown group dated around 64.92 Mya in the early Paleocene, and the East Asia–eastern North America or Eurasia–North America–Central America disjunct distribution patterns were primarily established during the middle Oligocene to Miocene. Conclusion The cryptic diversity found in this study indicates that the species diversity of lethal amanitas is strongly underestimated under the current taxonomy. The intercontinental sister species or sister groups relationships among East Asia and eastern North America or Eurasia–North America–Central America within lethal amanitas are best explained by the diversification model of Palaeotropical origin, dispersal via the Bering Land Bridge, followed by regional vicariance speciation resulting from climate change during the middle Oligocene to the present. These findings indicate the importance of both dispersal and vicariance in shaping the intercontinental distributions of these ectomycorrhizal fungi.
    BMC Evolutionary Biology 06/2014; 14(1):143. DOI:10.1186/1471-2148-14-143 · 3.37 Impact Factor
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