Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

BackgroundThe lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera.ResultsMost species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution.ConclusionAlthough DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.

[1]  S. Simard,et al.  Effects of clearcut logging and tree species composition on the diversity and community composition of epigeous fruit bodies formed by ectomycorrhizal fungi , 2006 .

[2]  D. Harris,et al.  Can you bank on GenBank , 2003 .

[3]  A. Dahlberg.  Community ecology of ectomycorrhizal fungi: an advancing interdisciplinary field , 2001 .

[4]  F. Nishida.  Key to the species of Inocybe in California , 1989 .

[5]  L. Tedersoo,et al.  Fine scale distribution of ectomycorrhizal fungi and roots across substrate layers including coarse woody debris in a mixed forest. , 2003, The New phytologist.

[6]  H. Nusbaum,et al.  Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria) , 2005, Molecular ecology.

[7]  B. Wang,et al.  Phylogenetic distribution and evolution of mycorrhizas in land plants , 2006, Mycorrhiza.

[8]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[9]  Robin Sen,et al.  UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. , 2005, The New phytologist.

[10]  S. Cameron,et al.  Are plant DNA barcodes a search for the Holy Grail? , 2006, Trends in ecology & evolution.

[11]  K. Nara.  Pioneer dwarf willow may facilitate tree succession by providing late colonizers with compatible ectomycorrhizal fungi in a primary successional volcanic desert. , 2006, The New phytologist.

[12]  oseph,et al.  How Should Species Phylogenies Be Inferred from Sequence Data? , 2001 .

[13]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[14]  Jos Houbraken,et al.  Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case , 2007, Proceedings of the National Academy of Sciences.

[15]  T. Kuyper.  A revision of the genus Inocybe in Europe I. Subgenus Inosperma and the smoothspored species of subgenus Inocybe. , 1986 .

[16]  W. Morris,et al.  CO2-enrichment and nutrient availability alter ectomycorrhizal fungal communities. , 2006, Ecology.

[17]  F. Richard,et al.  Diversity and specificity of ectomycorrhizal fungi retrieved from an old-growth Mediterranean forest dominated by Quercus ilex. , 2005, The New phytologist.

[18]  H. Brinkmann,et al.  Only a Few Fungal Species Dominate Highly Diverse Mycofloras Associated with the Common Reed , 2006, Applied and Environmental Microbiology.

[19]  J. Stangl.  Die Gattung Inocybe in Bayern , 1989 .

[20]  D. Hawksworth,et al.  Open letter to the scientific community of mycologists: provide voucher specimens. , 2000 .

[21]  E. Larsson,et al.  High phylogenetic diversity among corticioid homobasidiomycetes. , 2004, Mycological research.

[22]  R. Singer.  The Agaricales in modern taxonomy , 1949 .

[23]  Richard P. Shefferson,et al.  Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions , 2004 .

[24]  R. Molina,et al.  Douglas-fir ectomycorrhizae in 40- and 400-year-old stands: mycobiont availability to late successional western hemlock , 2005, Mycorrhiza.

[25]  T. McMahon,et al.  Updated world map of the Köppen-Geiger climate classification , 2007 .

[26]  A. Jumpponen,et al.  Fungal colonization of shrub willow roots at the forefront of a receding glacier , 2004, Mycorrhiza.

[27]  D. Hawksworth,et al.  Always deposit vouchers , 2000 .

[28]  J. Farris,et al.  PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING , 1996, Cladistics : the international journal of the Willi Hennig Society.

[29]  R. Turco,et al.  Nitrogen availability alters macrofungal basidiomycete community structure in optimally fertilized loblolly pine forests. , 2004, The New phytologist.

[30]  D. J. Lodge,et al.  Major clades of Agaricales: a multilocus phylogenetic overview , 2006, Mycologia.

[31]  M A Castellano,et al.  Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae). , 2001, American journal of botany.

[32]  J. Wendel,et al.  Ribosomal ITS sequences and plant phylogenetic inference. , 2003, Molecular phylogenetics and evolution.

[33]  T. Jeppesen,et al.  Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe. , 2007, Molecular phylogenetics and evolution.

[34]  T. Pennanen,et al.  Ectomycorrhizal community structure varies among Norway spruce (Picea abies) clones. , 2006, The New phytologist.

[35]  Mark Blaxter,et al.  Molecular barcodes for soil nematode identification , 2002, Molecular ecology.

[36]  D. Hawksworth,et al.  Open letter to the scientific community of mycologists: "Always deposit vouchers" , 2000, Mycorrhiza.

[37]  D. J. Funk,et al.  Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA , 2003 .

[38]  P. Kirk,et al.  Dictionary of the Fungi , 2008 .

[39]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[40]  Manolo Gouy,et al.  SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny , 1996, Comput. Appl. Biosci..

[41]  M. Garbelotto,et al.  A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis , 1998 .

[42]  P. Rygiewicz,et al.  Ectomycorrhizal fungi identification in single and pooled root samples: terminal restriction fragment length polymorphism (TRFLP) and morphotyping compared , 2005 .

[43]  T. Bruns,et al.  There is high potential for the formation of common mycorrhizal networks between understorey and canopy trees in a mixed evergreen forest , 2003 .

[44]  T. Bruns,et al.  Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest. , 2005, The New phytologist.

[45]  D. Berveiller,et al.  Mixotrophy in orchids: insights from a comparative study of green individuals and nonphotosynthetic individuals of Cephalanthera damasonium. , 2005, The New phytologist.

[46]  J. Cairney,et al.  Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sites , 2002 .

[47]  D. Hillis,et al.  Ribosomal DNA: Molecular Evolution and Phylogenetic Inference , 1991, The Quarterly Review of Biology.

[48]  D. Read,et al.  Changing partners in the dark: isotopic and molecular evidence of ectomycorrhizal liaisons between forest orchids and trees , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[49]  Introduction to Fungi , 1970 .

[50]  T. Kuyper,et al.  Vertical distribution of ectomycorrhizal fungal taxa in a podzol soil profile. , 2003, The New phytologist.

[51]  P. B. Matheny.  Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). , 2005, Molecular phylogenetics and evolution.

[52]  M. Buée,et al.  Year-round monitoring of diversity and potential metabolic activity of the ectomycorrhizal community in a beech (Fagus silvatica) forest subjected to two thinning regimes , 2005, Mycorrhiza.

[53]  J. Baar,et al.  Molecular analysis of ectomycorrhizal basidiomycete communities in a Pinus sylvestris L. stand reveals long-term increased diversity after removal of litter and humus layers. , 2003, FEMS microbiology ecology.

[54]  L. Tedersoo,et al.  Diversity and community structure of ectomycorrhizal fungi in a wooded meadow. , 2006, Mycological research.

[55]  M. Hershkovitz,et al.  Deep-level diagnostic value of the rDNA-ITS region. , 1996, Molecular biology and evolution.

[56]  J. Farris,et al.  Regular ArticlePARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING , 1996 .

[57]  M. Iotti,et al.  A quick and precise technique for identifying ectomycorrhizas by PCR. , 2006, Mycological research.

[58]  Liping Zhao,et al.  Dynamics of microbial community structure and cellulolytic activity in agricultural soil amended with two biofertilizers , 2005 .

[59]  T. Bruns,et al.  The molecular revolution in ectomycorrhizal ecology: peeking into the black‐box , 2001, Molecular ecology.

[60]  J. Rosselló,et al.  Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. , 2007, Molecular phylogenetics and evolution.

[61]  L. Koski,et al.  The Closest BLAST Hit Is Often Not the Nearest Neighbor , 2001, Journal of Molecular Evolution.

[62]  T. Henkel,et al.  New species of Inocybe from Dicymbe forests of Guyana. , 2003, Mycological research.

[63]  R. Henrik Nilsson,et al.  Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective , 2006, PloS one.

[64]  B. Rudolf,et al.  World Map of the Köppen-Geiger climate classification updated , 2006 .

[65]  M. Nei,et al.  Relationships between gene trees and species trees. , 1988, Molecular biology and evolution.

[66]  M. Wiemers,et al.  Does the DNA barcoding gap exist? – a case study in blue butterflies (Lepidoptera: Lycaenidae) , 2007, Frontiers in Zoology.

[67]  Anil K. Jain,et al.  Data clustering: a review , 1999, CSUR.

[68]  Takahito Kobayashi.  The taxonomic studies of the genus Inocybe , 2002 .

[69]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[70]  A. Vizzini,et al.  Morphological and molecular typing of the below-ground fungal community in a natural Tuber magnatum truffle-ground. , 2005, FEMS microbiology letters.

[71]  Andrew F. S. Taylor,et al.  Fungal communities in mycorrhizal roots of conifer seedlings in forest nurseries under different cultivation systems, assessed by morphotyping, direct sequencing and mycelial isolation , 2005, Mycorrhiza.

[72]  M. Weiß,et al.  Communities and populations of sebacinoid basidiomycetes associated with the achlorophyllous orchid Neottia nidus‐avis (L.) L.C.M. Rich. and neighbouring tree ectomycorrhizae , 2002, Molecular ecology.

[73]  J. Cairney,et al.  Influence of long-term repeated prescribed burning on mycelial communities of ectomycorrhizal fungi. , 2006, The New phytologist.

[74]  Rytas Vilgalys,et al.  Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples , 2005, Applied and Environmental Microbiology.

[75]  K. Nara.  Ectomycorrhizal networks and seedling establishment during early primary succession. , 2006, The New phytologist.

[76]  L. Tedersoo,et al.  Parallel evolutionary paths to mycoheterotrophy in understorey Ericaceae and Orchidaceae: ecological evidence for mixotrophy in Pyroleae , 2007, Oecologia.

[77]  R. Henrik Nilsson,et al.  Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi , 2005, BMC Bioinformatics.

[78]  S. Cheevadhanarak,et al.  Diversity of Ectomycorrhizal Fungi on Dipterocarpaceae in Thailand , 2006 .

[79]  Sally E Smith and David J Read.  Mycorrhizal Symbiosis 2nd ed , 1997 .

[80]  C. Meyer,et al.  The Controversy , 2022 .

[81]  R Henrik Nilsson,et al.  Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi). , 2005, Systematic biology.