Welcome to the Morchella MLST database. This dedicated database was set up at the CBS-KNAW Biodiversity Center by Vincent Robert in February 2012, using BioloMICS software (Robert et al., 2011), to facilitate DNA sequence-based identifications of Morchella species via the Internet. The current database is a natural extension of several multilocus molecular phylogenetic studies directed at assessing the genetic diversity and evolutionary relationships of true morels in Turkey and other regions of Europe (Taşkın et al., 2010, 2012), the P. R. China (Du et al., in review FGB), and worldwide (O’Donnell et al., 2011). To familiarize interested readers with the findings and methods employed in these investigations, PDFs of these studies are available for downloading from this site (see References Cited).
Morchella MLST has the following features
1) The database can be queried by keywords or using one of the two available identification tools. The first tool consists of a modified version of BLAST. Single sequences can be aligned against the reference database and ranked according to a combination of parameters including similarity, BLAST score, overlap percentage between query and reference sequences and number of fragments. The second tool is called polyphasic identification because it conducts pairwise alignments of one or several sequences from different loci at the same time. In the current version of the database, nucleotide BLAST queries can be conducted using DNA sequence data from one or more of the following five marker loci: ITS rDNA, and partial sequences of LSU rDNA, RPB1, RPB2, and EF-1 alpha.
2) Phenetic trees based on one of the following methods can also be constructed on the fly to help users locate the clade/species to which the unknown sequence belongs, via UPGMA, WPGMA, Single Linkage, Complete Linkage, UPGMC, WPGMC, Ward or Neighbor-Joining using a fixed model.
3) Sequences and NEXUS files of the alignments can be downloaded from this site so that users can conduct additional analyses.
Frequently Asked Questions (FAQs)
What are the main goals of Morchella MLST?
The two main objectives of Morchella MLST are to: 1) facilitate rapid and accurate identification of known and discovery of novel species worldwide via the Internet by archiving phylogenetic data, and 2) stimulate further studies (e.g., Baynes et al., 2011) by accessioning and distribution of DNA data and associated pure cultures to the research community.
What species are represented in Morchella MLST?
Multilocus DNA sequences of the 62 known phylogenetically distinct species are included in the current database. These species comprise the following three clades: Esculenta Clade (yellow morels, 27 species), Elata Clade (black morels, 34 species) and a monotypic Morchella rufobrunnea lineage (1 species). Herein we informally refer to a species-rich lineage comprising 22 species within the Elata Clade as the Elata Subclade (Du et al., in review FGB). Because Latin binomials can only be applied with confidence to one-third of the species (20/62), phylogenetic species within the Esculenta and Elata Clades are distinguished, respectively, by Mes (Mes-1-to-Mes-27) and Mel (Mel-1-to-Mel-34), followed by a unique Arabic number.
What locus or loci do you recommend for identifying unknowns?
ITS rDNA sequence data can be used to identify all of the known phylogenetic species within the Esculenta and Elata (Mel-1-to-10) Clades, except for the following closely related species pairs: Mes-23/Mes-24 and Mel-7/Mel-8 (Du et al., in review Mycologia). By contrast, only 10 of the 22 species within the Elata Subclade can be identified using ITS data. Multilocus sequence data is required to accurately identify the 12 other phylogenetic species within the Elata Subclade. Partial nucleotide sequences of the three protein-coding genes (RPB1, RPB2 and EF-1 alpha) also are useful for identifying most of the species within the Esculenta and Elata Clades. However, we do not recommend using sequences of the D1 and D2 domains of the LSU rDNA because it contains relatively little phylogenetic signal.
Can NCBI GenBank be used to identify unknowns to species?
Yes, but we recommend that you use sequences we deposited as a reference for each phylogenetic species: 1) because they were resolved as genealogically exclusive using multilocus DNA sequence data, and 2) because two-thirds of the Morchella ITS rDNA sequences identified to species in GenBank are misidentified (Du et al., in review Mycologia).
Why do some nucleotide BLAST queries of GenBank identify ITS rDNA sequences differently from Morchella MLST?
Our analyses of Morchella ITS rDNA sequences in GenBank revealed that at least 66% of the ones identified to species are misidentified (Du et al., in review).
How useful is emerencia (http://www.emerencia.org) for determining the taxonomic affiliation of Morchella ITS rDNA sequences in GenBank?
Emerencia cannot be used to obtain reliable species identifications for Morchella because two-thirds of the ‘fully identified sequences’ (i.e., ones with binomials) it retrieved from GenBank as a reference are misidentified.
Are Morchella species cosmopolitan in their distribution?
No. Contrary to the tacit assumption made in field guides, most Morchella species exhibit high continental endemism and provincialism in the Northern Hemisphere (O’Donnell et al., 2011). This phylogenetic knowledge is important in formulating sound conservation policies directed at protecting and preserving morel genetic diversity in the areas sampled, and promoting informed management practices that help insure the sustainability of commercial harvests. Given the restricted geographic distribution of most species, targeting poorly sampled areas for future studies should greatly expand our knowledge of their genetic diversity and geographic distribution.
How can someone contribute to Morchella MLST?
Researchers are encouraged to deposit sequences, trace chromatograms, cultures and associated collection data in the database.
Baynes, M. A., Newcombe, G., Dixon, L., Castlebury, L. and O’Donnell, K. 2011. A novel plant-fungal mutualism associated with fire. Fungal Biol. doi:10.1016/j.funbio.2011.10.008.
Du, X.-H., Zhao, Q., O’Donnell, K., Rooney, A. P. and Yang, Z. L. Multigene molecular phylogenetics reveals true morels (Morchella) are especially species-rich in China. Fungal Genet. Biol. (in review).
Du, X.-H., Zhao, Q., Yang, Z. L., Hansen, K., Taşkın, H., Büyükalaca, S., Dewsbury, D., Moncalvo, J.-M., Douhan, G. W., Robert, V. A. R. G., Crous, P. W., Rehner, S. A., Rooney, A. P., Sink S. and O’Donnell, K. How well do ITS rDNA sequences differentiate species of true morels (Morchella)? Mycologia (in review).
O’Donnell, K., Rooney, A. P., Mills, G. L., Kuo, M., Weber, N. S. and Rehner, S. A. 2011. Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic . Fungal Genet. Biol. 48:252–265.
Robert, V., Szoke, S., Jabas, J., Vu, D., Chouchen, O., Blom, E. and Cardinali, G. 2011. BioloMICS software, Biological data Management, Identification, Classification and Statistics. The Open Applied Informatics Journal 5:87–98.
Taşkın, H., Büyükalaca, S., Doğan, H. H., Rehner, S. A. and O’Donnell, K. 2010. A multigene molecular phylogenetic assessment of true morels (Morchella) in Turkey . Fungal Genet. Biol. 47:672–682.
Taşkın, H., Büyükalaca, S., Hansen, K. and O’Donnell, K. Multilocus phylogenetics analysis of true morels (Morchella) reveals high levels of endemics in Turkey relative to other regions of Europe. 2012. Mycologia doi:10.3852/11–180.
A number of multiple alignments (NEXUS files) have been used for the above publications and can be downloaded here.