Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)
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Erik Kristiansson | Martin Ryberg | Mats Töpel | R Henrik Nilsson | Ellen Larsson | E. Kristiansson | E. Larsson | R. H. Nilsson | M. Ryberg | M. Töpel | Stig Jacobsson | S. Jacobsson | R. Nilsson
[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.