Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project

Abstract

Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1–2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.

Recent advances in population genetics of ectomycorrhizal mushroomsRussulaspp.

“…Recent researches investigated the ectomycorrhizal fungal species in tropical zones and found abundant ectomycorrhizal fungal communities below the ground (Buyck et al 1996; Lee et al 1997; Riviere et al 2007; Phosri et al 2012; Osmundson et al 2013). Indeed, species in family Russulaceae are now considered one of the most dominant ectomycorrhizal fungal groups in the tropics.…”

“…Indeed, species in family Russulaceae are now considered one of the most dominant ectomycorrhizal fungal groups in the tropics. Many novel species of Russula have been reported recently from tropical zones (Riviere et al 2007; Phosri et al 2012; Osmundson et al 2013). The type genus Russula is the most specious genus in family Russulaceae and was first established based on the studies of macro fungi in northern Europe.…”

“…Globally, about 750 species have been recorded in this genus (Kirk et al 2008). Some Russula species (e.g., Russula nigricans and Russula pectinatoides ) are found in several continents (Eberhardt 2002; Miller and Buyck 2002; Shimono et al 2004; Ashkannejhad and Horton 2006; Palmer et al 2008; Yin et al 2008; Jones et al 2012; Osmundson et al 2013; Park et al 2014), whereas others show geographic specific distributions (e.g., Russula brevipes is mainly distributed in North America, Russula ochroleuca is mainly distributed in Europe, and Russula discopus is dominated in tropical zone) (Bergemann and Miller 2002; Eberhardt 2002; Miller and Buyck 2002; Riviere et al 2007; Kellner et al 2009; Kottke et al 2010; Kleine et al 2013; Osmundson et al 2013). Over the past decade, biodiversity surveys using new molecular methods and/or analyzing previously under-surveyed territories and ecological niches have led to the discovery of many new species in this genus, such as Russula changbaiensis (northeast China), Russula tsokae (Sikkim, Himalayas), Russula galbana (Australasia), and Russula caeruleoanulata (west Africa) (Lebel and Tonkin 2007; Douanla-Meli and Langer 2009; Das et al 2010; Li et al 2013).…”

The genus Podaxis in arid regions of Mexico: preliminary ITS phylogeny and ethnomycological use

“…The newly obtained ITS sequences (Table 1) were aligned with ITS sequences of authenticated published sequences or from vouchered fungarium samples (Brock et al 2009;Osmundson et al 2013), such as those from a recent phylogenetic study on Podaxis spp. (Conlon et al 2016) using the multiple sequence alignment program MUSCLE (Edgar 2004), with default parameters in operation.…”

Coprinopsis rugosomagnispora: a distinct new coprinoid species from Poland (Central Europe)

“…are demarcated with colored squares, and three Agrocybe species were included as outgroup. The species assigned to the so-called Atramentarii clade by Nagy et al (2013a) are demarcated within lineage containing species showing characters of the morphological subsection Lanatuli experts of Coprinopsis taxonomy (Keirle et al 2004;Navarro-González et al 2006;Garcia and Vellinga 2010;Nagy et al 2010aNagy et al , 2011Nagy et al , 2013aGeml et al 2012;Osmundson et al 2013;Ruiz et al 2013;Ö rstadius et al 2015;Elwess et al 2016; and some unpublished sequences available in GenBank). A total of 85 sequences were aligned using MUSCLE algorithm and default settings (Edgar 2004) to obtain preliminary hypothesis on the phylogenetic placement of Coprinopsis rugosomagnispora (data not shown).…”