-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
2
-
-
34547197374
-
Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR
-
Arnold, A.E. et al. (2007) Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia, 99, 185-206.
-
(2007)
Mycologia
, vol.99
, pp. 185-206
-
-
Arnold, A.E.1
-
3
-
-
68149135199
-
A phylogenetic estimation of trophic transition networks for ascomycetous fungi: Are lichens cradles of symbiotrophic fungal diversification?
-
Arnold, A.E. et al. (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst. Biol., 58, 283-297.
-
(2009)
Syst. Biol.
, vol.58
, pp. 283-297
-
-
Arnold, A.E.1
-
4
-
-
84928914690
-
Continental-scale distributions of dust-associated bacteria and fungi
-
Barberán, A. et al. (2015) Continental-scale distributions of dust-associated bacteria and fungi. Proc. Natl. Acad. Sci. U. S. A., 112, 5756-5761.
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. 5756-5761
-
-
Barberán, A.1
-
5
-
-
79955456912
-
Performance accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood
-
Berger, S.A. et al. (2011) Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol., 60, 291-302.
-
(2011)
Syst. Biol.
, vol.60
, pp. 291-302
-
-
Berger, S.A.1
-
6
-
-
79960414804
-
Aligning short reads to reference alignments and trees
-
Berger, S.A. and Stamatakis, A. (2011) Aligning short reads to reference alignments and trees. Bioinformatics, 27, 2068-2075.
-
(2011)
Bioinformatics
, vol.27
, pp. 2068-2075
-
-
Berger, S.A.1
Stamatakis, A.2
-
7
-
-
79952741082
-
The fungi: 1, 2, 3. 5.1 million species?
-
Blackwell, M. (2011) The fungi: 1, 2, 3. 5.1 million species? Am. J. Bot., 98, 426-438.
-
(2011)
Am. J. Bot.
, vol.98
, pp. 426-438
-
-
Blackwell, M.1
-
8
-
-
67650757433
-
TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutierrez, S. et al. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutierrez, S.1
-
9
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J.G. et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 7, 335-336.
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
10
-
-
84923687625
-
Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales eurotiales, and a new order ?phaeomoniellales
-
Chen, K.H. et al. (2015) Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order -Phaeomoniellales. Mol. Phylogenet. Evol., 85, 117-130.
-
(2015)
Mol. Phylogenet. Evol.
, vol.85
, pp. 117-130
-
-
Chen, K.H.1
-
11
-
-
84938696821
-
Identifying and naming plant-pathogenic fungi: Past present, and future
-
Crous, P.W. et al. (2015) Identifying and naming plant-pathogenic fungi: past, present, and future. Annu. Rev. Phytopathol., 53, 247-267.
-
(2015)
Annu. Rev. Phytopathol.
, vol.53
, pp. 247-267
-
-
Crous, P.W.1
-
12
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
13
-
-
0027580147
-
ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts
-
Gardes, M. and Bruns, T.D. (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol. Ecol., 2, 113-118.
-
(1993)
Mol. Ecol.
, vol.2
, pp. 113-118
-
-
Gardes, M.1
Bruns, T.D.2
-
14
-
-
84858081642
-
Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota)
-
Gaya, E. et al. (2012) Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota). Mol. Phylogenet. Evol., 63, 374-387.
-
(2012)
Mol. Phylogenet. Evol.
, vol.63
, pp. 374-387
-
-
Gaya, E.1
-
15
-
-
84955402784
-
The genome of Xylona heveae provides a window into fungal endophytism
-
Gazis, R. et al. (2016) The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol., 120, 26-42.
-
(2016)
Fungal Biol.
, vol.120
, pp. 26-42
-
-
Gazis, R.1
-
16
-
-
84864572814
-
Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes
-
Gazis, R. et al. (2012) Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes. Mol. Phylogenet. Evol., 65, 294-304.
-
(2012)
Mol. Phylogenet. Evol.
, vol.65
, pp. 294-304
-
-
Gazis, R.1
-
17
-
-
0004152299
-
The fungal dimension of biodiversity: Magnitude significance, and conservation
-
Hawksworth, D.L. (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol. Res., 95, 641-655.
-
(1991)
Mycol. Res.
, vol.95
, pp. 641-655
-
-
Hawksworth, D.L.1
-
18
-
-
0035712954
-
The magnitude of fungal biodiversity: The 1.5 million species estimate revisited
-
Hawksworth, D.L. (2001) The magnitude of fungal biodiversity: the 1.5 million species estimate revisited. Mycol. Res., 105, 1422-1432.
-
(2001)
Mycol. Res.
, vol.105
, pp. 1422-1432
-
-
Hawksworth, D.L.1
-
19
-
-
34250341823
-
A higher-level phylogenetic classification of the Fungi
-
Hibbett, D.S. et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol. Res., 111, 509-547.
-
(2007)
Mycol. Res.
, vol.111
, pp. 509-547
-
-
Hibbett, D.S.1
-
20
-
-
33750329972
-
Reconstructing the early evolution of Fungi using a six-gene phylogeny
-
James, T.Y. et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature, 443, 818-822.
-
(2006)
Nature
, vol.443
, pp. 818-822
-
-
James, T.Y.1
-
21
-
-
77955019084
-
Parallelization of the MAFFT multiple sequence alignment program
-
Katoh, K. and Toh, H. (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics, 26, 1899-1900.
-
(2010)
Bioinformatics
, vol.26
, pp. 1899-1900
-
-
Katoh, K.1
Toh, H.2
-
22
-
-
84892984482
-
Ion Torrent PGM as tool for fungal community analysis: A case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
-
Kemler, M. et al. (2013) Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity. PLoS One, 8, e81718.
-
(2013)
PLoS One
, vol.8
, pp. e81718
-
-
Kemler, M.1
-
23
-
-
35148836940
-
Ainsworth & bisby's dictionary of the fungi
-
10th edn., Wallingford, UK
-
Kirk, P.M. et al. (2008) Ainsworth & Bisby's Dictionary of the Fungi. 10th edn. Cabi Series. CAB International, Wallingford, UK.
-
(2008)
Cabi Series. CAB International
-
-
Kirk, P.M.1
-
24
-
-
84886099720
-
Towards a unified paradigm for sequence-based identification of fungi
-
Koljalg, U. et al. (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol., 22, 5271-5277.
-
(2013)
Mol. Ecol.
, vol.22
, pp. 5271-5277
-
-
Koljalg, U.1
-
25
-
-
0034351388
-
Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology
-
Lutzoni, F. et al. (2000) Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst. Biol., 49, 628-651.
-
(2000)
Syst. Biol.
, vol.49
, pp. 628-651
-
-
Lutzoni, F.1
-
27
-
-
84938216363
-
Fungal endophytes in aboveground tissues of desert plants: Infrequent in culture but highly diverse and distinctive symbionts
-
Massimo, N.C. et al. (2015) Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts. Microb. Ecol., 70, 61-76.
-
(2015)
Microb. Ecol.
, vol.70
, pp. 61-76
-
-
Massimo, N.C.1
-
28
-
-
77958610660
-
Pplacer: Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
-
Matsen, F.A. et al. (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 538
-
-
Matsen, F.A.1
-
29
-
-
0038339411
-
A predatory fungus (Hyphomycetes: Lecophagus) attacking Rotifera and Tardigrada in maritime Antarctic lakes
-
McInnes, S.J. (2003) A predatory fungus (Hyphomycetes: Lecophagus) attacking Rotifera and Tardigrada in maritime Antarctic lakes. Polar Biol., 26, 79-82.
-
(2003)
Polar Biol.
, vol.26
, pp. 79-82
-
-
McInnes, S.J.1
-
30
-
-
34247580695
-
New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes
-
Miadlikowska, J. et al. (2006) New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia, 98, 1088-1103.
-
(2006)
Mycologia
, vol.98
, pp. 1088-1103
-
-
Miadlikowska, J.1
-
31
-
-
84904124689
-
A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa 317 genera and 66 families
-
Miadlikowska, J. et al. (2014) A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. Mol. Phylogenet. Evol., 79, 132-168.
-
(2014)
Mol. Phylogenet. Evol.
, vol.79
, pp. 132-168
-
-
Miadlikowska, J.1
-
32
-
-
84927624720
-
A RESTful API for access to phylogenetic tools via the CIPRES science gateway
-
Miller, M.A. et al. (2015) A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol. Bioinform. Online, 11, 43-48.
-
(2015)
Evol. Bioinform. Online
, vol.11
, pp. 43-48
-
-
Miller, M.A.1
-
33
-
-
25144516095
-
Fungal community analysis by large-scale sequencing of environmental samples
-
O'Brien, H.E. et al. (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl. Environ. Microbiol., 71, 5544-5550.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 5544-5550
-
-
O'Brien, H.E.1
-
34
-
-
84879434377
-
Illumina metabarcoding of a soil fungal community
-
Schmidt, P.A. et al. (2013) Illumina metabarcoding of a soil fungal community. Soil Biol. Biochem., 65, 128-132.
-
(2013)
Soil Biol. Biochem.
, vol.65
, pp. 128-132
-
-
Schmidt, P.A.1
-
35
-
-
67749119915
-
The Ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits
-
Schoch, C.L. et al. (2009) The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst. Biol., 58, 224-239.
-
(2009)
Syst. Biol.
, vol.58
, pp. 224-239
-
-
Schoch, C.L.1
-
36
-
-
34247558477
-
A five-gene phylogeny of Pezizomycotina
-
Spatafora, J.W. et al. (2006) A five-gene phylogeny of Pezizomycotina. Mycologia, 98, 1018-1028.
-
(2006)
Mycologia
, vol.98
, pp. 1018-1028
-
-
Spatafora, J.W.1
-
37
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
38
-
-
84914142313
-
Fungal biogeography. Global diversity and geography of soil fungi
-
Tedersoo, L. et al. (2014) Fungal biogeography. Global diversity and geography of soil fungi. Science, 346, 1256688.
-
(2014)
Science
, vol.346
, pp. 1256688
-
-
Tedersoo, L.1
-
39
-
-
63049115867
-
Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: A case study for analysing fungal environmental samples
-
U'Ren, J.M. et al. (2009) Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples. Mycol. Res., 113, 432-449.
-
(2009)
Mycol. Res.
, vol.113
, pp. 432-449
-
-
U'Ren, J.M.1
-
40
-
-
77956877597
-
Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens
-
U'Ren, J.M. et al. (2010) Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens. Microb. Ecol., 60, 340-353.
-
(2010)
Microb. Ecol.
, vol.60
, pp. 340-353
-
-
U'Ren, J.M.1
-
41
-
-
84860550454
-
Host and geographic structure of endophytic and endolichenic fungi at a continental scale
-
U'Ren, J.M. et al. (2012) Host and geographic structure of endophytic and endolichenic fungi at a continental scale. Am. J. Bot., 99, 898-914.
-
(2012)
Am. J. Bot.
, vol.99
, pp. 898-914
-
-
U'Ren, J.M.1
-
42
-
-
84959351171
-
Contributions of North American endophytes to the phylogeny ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)
-
U'Ren, J.M. et al. (2016) Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Mol. Phylogenet. Evol., 98, 210-232.
-
(2016)
Mol. Phylogenet. Evol.
, vol.98
, pp. 210-232
-
-
U'Ren, J.M.1
-
43
-
-
84905995464
-
Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi
-
U'Ren, J.M. et al. (2014) Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi. Mol. Ecol. Resour., 14, 1032-1048.
-
(2014)
Mol. Ecol. Resour.
, vol.14
, pp. 1032-1048
-
-
U'Ren, J.M.1
-
44
-
-
0025374564
-
Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species
-
Vilgalys, R. and Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol., 172, 4238-4246.
-
(1990)
J. Bacteriol.
, vol.172
, pp. 4238-4246
-
-
Vilgalys, R.1
Hester, M.2
-
45
-
-
0000432452
-
Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
-
L Innis, M. et al. (eds), Academic Press, Orlando, Florida
-
White, T.J. et al. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. InL Innis, M. et al. (eds) PCR Protocols: A Guide toMethods and Applications. Academic Press, Orlando, Florida, pp. 315-322.
-
(1990)
PCR Protocols: A Guide ToMethods and Applications
, pp. 315-322
-
-
White, T.J.1
-
46
-
-
84864680957
-
Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape
-
Zimmerman, N.B. and Vitousek, P.M. (2012) Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. Proc. Natl. Acad. Sci. U. S. A., 109, 13022-13027.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 13022-13027
-
-
Zimmerman, N.B.1
Vitousek, P.M.2
|