How well do ITS rDNA sequences differentiate species of true morels (Morchella)?

Authors: DU, XI-HUI - Chinese Academy Of Sciences; ZHAO, QI - Chinese Academy Of Sciences; YANG, ZHU - Chinese Academy Of Sciences; HANSEN, KAREN - The Swedish Museum Of Natural History; TASKIN, HATIRA - Cukurova University; BUYUKALACA, SAADET - Cukurova University; DEWSBURY, DAMON - University Of Toronto; MONCALVO, JEAN-MARC - University Of Toronto; DOUHAN, GREG - University Of California; ROBERT, VINCENT - Fungal Biodiversity; CROUS, PEDRO - Fungal Biodiversity; Rehner, Stephen; Rooney, Alejandro - Alex; Sink, Stacy; O Donnell, Kerry

Submitted to: Mycologia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2012
Publication Date: 11/1/2012
Citation: Du, X., Zhao, Q., Yang, Z.L., Hansen, K., Taskin, H., Buyukalaca, S., Dewsbury, D., Moncalvo, J., Douhan, G.Q., Robert, V.A., Crous, P.W., Rehner, S.A., Rooney, A.P., Sink, S.L., O'Donnell, K. 2012. How well do ITS rDNA sequences differentiate species of true morels (Morchella)? Mycologia. 104(6):1351-1368.

Interpretive Summary: Commercial harvesting of morels has grown into highly lucrative cottage industries in several morel-rich countries, including China, Turkey and the United States. Due to the increasing commercial demand, it is imperative that comprehensive studies are conducted in order to develop informed science-based conservation policies and management practices that will ensure that species diversity is maximally preserved and commercial harvests are sustainable. Towards this end, we assessed the utility of internal transcribed spacer (ITS) rDNA sequence data for identifying species so that their geographic distribution and area of endemism can be critically assessed and so that previously unknown species can be detected and identified for further genetic evaluation. Herein we mined ITS sequences in the GenBank database to better understand species diversity and their geographic distributions. To facilitate DNA typing of strains and collections via the Internet, we develop a dedicated, web-accessible informational database called Morchella multilocus sequence typing (MLST) (http://www.cbs.knaw.nl/morchella/) that facilitates DNA sequence-based identifications of true morels via the web. We populated Morchella MLST with DNA sequence data generated in the current and our prior multilocus molecular genetic studies of this economically important group of highly prized edible fungi. Pure cultures of diverse morel species were made and are stored in the ARS Culture Collection to benefit biotechnologists interested in cultivating morels commercially. Finally, the results of this study provide invaluable information needed to develop appropriate practices for the conservation and sustainable harvest of morels.

Technical Abstract: Arguably more mycophiles hunt true morels (Morchella) during their brief fruiting season each spring in the Northern Hemisphere than any other wild edible fungus. Concerns about overharvesting by individual collectors and commercial enterprises make it essential that science-based management practices and conservation policies are developed to insure the sustainability of commercial harvests and to protect and preserve morel species diversity. Therefore, the primary objectives of the present study were to: (i) investigate the utility of the ITS rDNA fungal ‘barcode’ locus for identifying Morchella species, using phylogenetic species previously identified inferred from multilocus DNA sequence data as a reference; and (ii) identify ‘insufficiently identified’ sequences and determine whether the named sequences in GenBank were identified correctly. Towards this end, we generated 660 Morchella ITS rDNA sequences and downloaded 246 additional ones generated by other researchers from GenBank using emerencia (http://www.emerencia.org) and analyzed them phylogenetically. Three major findings emerged: (i) internal transcribed spacer (ITS) rDNA sequences were useful in identifying 47/62 (75.8%) of the known phylospecies; however, they failed to identify 12 of the 22 species within the species-rich Elata Subclade, and two closely related species in the Esculenta Clade; (ii) at least 66% of the named Morchella sequences in GenBank are misidentified; and (iii) ITS rDNA sequences of up to six putatively novel Morchella species were represented in GenBank. Recognizing the need for a dedicated web-accessible reference database to facilitate the rapid identification of known and novel species, we constructed Morchella MLST (http://www.cbs.knaw.nl/morchella/) which can be queried using ITS rDNA sequences and those of the four other genes used in our prior multilocus molecular systematic studies of this charismatic genus.