메뉴 건너뛰기




Volumn 33, Issue 8, 2017, Pages 1160-1168

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: An example with the Pezizomycotina tree of life

Author keywords

[No Author keywords available]

Indexed keywords

ASCOMYCETES; ENDOPHYTE; GENE LOCUS; GENETICS; METADATA; PHYLOGENY; PHYSIOLOGY; PROCEDURES; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 85019162418     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw808     Document Type: Article
Times cited : (50)

References (46)
  • 1
    • 0025183708 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.