What’s for dinner? Undescribed species of porcini in a commercial packet

Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.


INTRODUCTION
Kingdom Fungi is one of the most diverse groups of eukaryotes with estimates ranging from 500,000 to nearly 10 million species, yet they remain vastly underdocumented (Bass & Richards, 2011).Present rates of description, which add on average about 1,200 new species annually (Hibbett et al., 2011), are grossly inadequate for the task.Given that human society has derived tremendous benefit from the foods, medicines, and ecological services provided by as little as 1% of the fungi we know of, the impact of this missing diversity on human livelihoods is potentially profound.Importantly, this missing diversity is not just restricted to remote, underexplored regions of the world, but is a pervasive phenomenon where even our foods can harbor unknown species.
Although taxonomists regard new fungal taxa as commonplace, they are often of little apparent consequence to human society and largely go unnoticed by the public.Like all groups of organisms, our knowledge of fungal diversity is biased towards taxa of greatest concern to ourselves, such as edible fungi.For example, wild mushrooms collected and sold as food around the world generally belong to a handful of well-known taxa (e.g., truffles and chanterelles), most of which have long histories of use in European cuisine.However, even some of these well-known groups have been shown to contain underappreciated levels of diversity.One of these, porcini, has recently been shown to be far more diverse than previously thought (Dentinger et al., 2010;Feng et al., 2012), suggesting the potential for unknown species to end up in the international food supply chain.Although no porcini are known to be poisonous, food allergens have been reported from them (Torricelli, Johansson & Wütrich, 1997;Helbling et al., 2002;Castillo et al., 2013).Therefore, insufficient knowledge of the porcini species contained in food products could pose a health concern.
Porcini are estimated to have an annual worldwide consumption up to 100,000 metric tons (Hall et al., 1998).However, their harvest is restricted to wild foraging since, to date, their cultivation has failed.The high prices for this wild food foraged locally in Europe and North America has driven the market towards less costly sources, such as China (Sitta & Floriani, 2008).According to the official website of Yunnan Province (www.yunnan.cn), the major exporter of wild mushrooms in China, locally-sourced porcini have been exported to Europe since 1973, and mushrooms of Chinese origin now account for approximately half of all dried porcini in Italy (Sitta & Floriani, 2008).The Chinese species of porcini have been shown previously to be more closely related to European Boletus aereus than they are to the core commercial species, B. edulis, with which they last shared a common ancestor up to ∼56 million years ago (Dentinger et al., 2010;Feng et al., 2012).
Given what was previously known about the commercial porcini originating in China, we hypothesized that the contents of a commercially available packet of porcini in the UK would contain multiple species.We set out to rapidly diagnose these species using molecular-based 'turbo-taxonomy' (Butcher et al., 2012) that employs a combination of modern tools and approaches.Our results show that, with a combination of phylogenetic taxonomy and e-published nomenclature, three previously unnamed species of porcini could be quickly recognized and formally named from a single packet sold in a London grocer.

MATERIAL AND METHODS
A packet of dried porcini was purchased from a grocer in southwest greater London in October 2013.Fifteen pieces of mushroom were removed arbitrarily from the packet and DNA was extracted using the Sigma Extract-N-Amp kit.The full ITS region of the nrDNA was PCR-amplified using primers ITS1F and ITS4 (White et al., 1990;Gardes & Bruns, 1993).Successful amplicons were purified using ExoSAP-IT (USB, Cleveland, OH) and sequenced bidirectionally using BigDye3.1 with an ABI 3730 (Applied Biosystems, Foster City, CA).Complementary unidirectional reads were aligned and edited using Sequencher 4.2 (GeneCodes, Ann Arbor, MI).

RESULTS AND DISCUSSION
The GMYC model with the greatest significant ML score included three ML clusters (1-10 clusters with 95% confidence) plus the root (4 ML entities; 2-23 with 95% confidence).GMYC supports for the three ML clusters were weak, low bGMYC posterior probabilities indicated a substantial level of phylogenetic uncertainty, while the maximum likelihood bootstraps supported reciprocal monophyly (79%, 76% and 100% for each cluster respectively; Fig. 1).Percent sequence similarity did not support distinction between Figure 1 Phylogeny and alignment of three unnamed species discovered in a commercial packet of dried porcini.On the left is an ultrametric tree rooted with Boletus aereus and with branch lengths transformed using the uncorrelated relaxed clock model in BEAST.The relationship of the core species or porcini, Boletus edulis, to the dataset is depicted using a dashed line.Clades with dark red branches represent the three maximum likelihood clusters in the GMYC model with the greatest ML score calculated using the single method in the 'splits' package in R. Terminal labels in blue represent sequences derived from individual pieces of mushroom sampled from a commercial packet of porcini.Pie charts on branches show maximum likelihood bootstraps ('MLBS'; lightest red), GMYC supports ('GMYC'; medium red), and posterior probabilities of the cluster as calculated using bGMYC ('bGMYC'; darkest red).On the right is the alignment exported from Mesquite v2.75 (Maddison & Maddison, 2011) of 34 variable positions in the ITS region after excluding uninformative sites using PAUP* (Swofford, 2002).Nucleotide characters are depicted using IUPAC codes, gaps depicted by a '-' and ambiguous/missing data depicted by '?' .
any of the three species detected by GMYC and bootstrapping, where the minimum uncorrected pairwise distances between clades was greater than the maximum uncorrected pairwise distances within clades (Table 1).This result suggests that, while GMYC may be particularly sensitive to phylogenetic uncertainty as revealed by the low support values, for this dataset it performs better at diagnosing phylogenetic units than the commonly used percent similarity threshold of 97% (e.g., O'Brien et al., 2005).The phylogenetic uncertainty observed is almost certainly caused by a high ratio of parsimony uninformative variable sites (60 variable positions, 34 parsimony uninformative) to phylogenetically informative changes (26 positions).Of the informative characters, only 11 of them correspond to variable positions between the two closest taxa, B. bainiugan and B. meiweiniuganjun, with five sequences showing heterozygous bases at 6 positions (possibly due to incomplete lineage sorting) and only three of these corresponding to synapomorphic substitutions (Fig. 1).Five sequences contained autapomorphic substitutions in 18 positions, representing more than half of all parsimony uninformative characters, with up to 9 autapomorphies occurring in a single sequence (JN563917).These autapomorphies translate into longer terminal branch lengths relative to internal nodes, which reduces the distinction of within and between cluster branching patterns, a phenomenon that is known to affect GMYC supports (Fujisawa & Barraclough, 2013).These substitutions may indicate true variation in the ITS region, yet 94% come from Table 1 Intra-and inter-specific uncorrected ITS barcode sequence distances of the three unnamed species discovered in a commercial packet of dried porcini.Ranges are minimum-maximum distances expressed as percent.

B. bainiugan B. meiweiniuganjun B. shiyong
Boletus bainuigan 0-2.2 B. meiweiniuganjun 0.4-3.30-1.5 B. shiyong 1.9-4.21.5-3.30-3.6 sequences downloaded from GenBank, with only two sequences (JN563906, JN563917) contributing 83% of the autapomorphies.We suspect that, rather than true variation, these substitutions may instead be the result of sequencing and editing errors.Such errors can have large impacts on phylogenetic inference when the number of phylogenetically informative sites is small, such as in ITS sequences of recently diverged fungi, underscoring the importance of careful scrutiny during sequence preparation.Three species could be identified based on corroboration of ML-supported reciprocal monophyly and GMYC clustering, and these corresponded to lineages previously reported in phylogenetic analyses (Dentinger et al., 2010;Feng et al., 2012;Sitta & Floriani, 2008), but none of which were formally named or described.Review of recent treatments of Chinese boletes also did not provide names for these taxa, which have been treated as a handful of species that occur in Europe and North America (Zang, 2006).New names were formally published on 12 October 2013 (see http://www.indexfungorum.org/Publications/Index%20Fungorum%20no.29.pdf for terse descriptions, 1 voucher information, and GenBank 1 The numbers reported in the original descriptions should be multiplied by 2.43 to achieve correct measurements of cells and spores.accessions corresponding to these taxa).We hope that by naming these taxa and providing reference sequences for comparison, we will encourage mycologists with ready access to fresh collections of these species to record and document their characteristics and discover new features that may help to distinguish them.
Together with improvements in single-locus diagnosis leading to more robust inferences of evolutionary significant units (Butcher et al., 2012), rapid survey and diagnosis of vast communities of undescribed diversity is initiating a revolution in taxonomy (Riedel et al., 2013).This is particularly true for Fungi, which are hyperdiverse and largely cryptic, requiring indirect detection with environmental sequencing for documenting their true diversity (Taylor et al., 2014;Lücking et al., 2014).As a consequence, a vast quantity of fungal diversity is only known from DNA sequences, and these are accumulating in public databases at incredibly rapid rates (Hibbett et al., 2011).Although recent attempts to accelerate species description using short, unique DNA sequences 'DNA barcoding' (Hebert et al., 2003) and rapid, short description 'turbo-taxonomy' (Butcher et al., 2012) hold promise for meeting the enormous challenge of documenting hyperdiverse and largely unknown groups of organisms (Riedel et al., 2013), they still remain marginal to traditional methods for formal diagnosis of fungal diversity.
Turbo-taxonomy is an important improvement to efficiency in reconciling molecular diagnosis with a standard application of names that enable universal communication about biodiversity.Together, DNA sequence-based diagnosis and turbo-taxonomy catalyze description of new species, thereby greatly accelerating the rate at which diversity can be documented and recognized.Although descriptions based on features of organisms that are readily observed without specialized techniques are ideal, this is not always possible and descriptions based on features of DNA sequences could be automated to satisfy rules on naming.Automated pipelines that integrate analysis, taxonomy, and nomenclature will soon accelerate this revolution, enabling us to capture the most comprehensive baseline information on global organismal diversity possible.Given estimated rates of species extinction from 0.1 to 5% per year (Costello, May & Stork, 2013), and using recent estimates of global fungal diversity of ∼6 million species (Taylor et al., 2014), extinction rates may exceed description rates in Fungi by up to 5 times.An 'integrative fast track' approach (Riedel et al., 2013) offers the only tractable solution presently available to filling this knowledge gap.And as has been shown here with the three new species of porcini in a widely available commercial product, this knowledge gap can and does have direct impacts on our lives.

CONCLUSIONS
Our analysis of 15 pieces of dried porcini mushrooms from a single commercial packet showed three species corresponding to lineages that although previously reported in phylogenetic analyses have never been formally named or described until now.The recognition of these species enables them to be monitored in foods and facilitates countries' adherence to international agreements on exploitation of wildlife, i.e., the Convention on Biological Diversity.