Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

By F. Lutzoni, Frank Kauff, C. Cox, D. McLaughlin, G. Celio, Bryn T. M. Dentinger, M. Padamsee, D. Hibbett, Timothy Y. James, E. Baloch and 34 more. American-Eurasian journal of botany, 2004

821 citations recorded by the source corpus.

Subfields: Cell Biology, Ecology, Evolution, Behavior and Systematics, Plant Science

View Paper: https://www.semanticscholar.org/paper/3c5a18a03ad1c0f0c7f61b4f2dda15be1a12fbd6

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Citations in the corpus

Fire severity influences the response of soil microbes to a boreal forest fire (2016, methodology): “For reference-based chimera detection, we used a manually curated database of 18S sequences of fungi submitted to GenBank as part of the Assembling the Fungal Tree of Life (AFTOL) project (Lutzoni et al 2004).”
Fungi in lake ecosystems (2010, background): “Only recently has a consistent fungal tree of life been generated (Lutzoni et al. 2004, James et al. 2006), and it excludes several phylogenetic groups formerly considered fungi, e.g. Oomycetes and various slime molds.”
Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies (2014, background): “Additionally, lichenised species also appeared to be nested within Dothideomycetes (Lutzoni et al. 2004; James et al. 2006; Del Prado et al. 2006; Muggia et al. 2008; 2013; Nelsen et al. 2009).”
Families of Dothideomycetes (2013, background): “…2001; Liu and Hall 2004), although several lineages previously assigned to that group, such as the Pyrenulales and Verrucariales , are now classified in subclass Chaetothyriomycetidae, class Eurotiomycetes (Lutzoni et al. 2004; Schmitt et al. 2005; Hibbett et al. 2007; Schoch et al. 2009a, b).”
The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota – Approaching one thousand genera (2016, background): “Initially, studies focused on broad fungal phylogenies, shaping the backbone of both the Ascomycota and Basidiomycota into major lineages later recognized as subphyla and classes (Hibbett et al. 2007; Lutzoni et al. 2004; Schoch et al. 2009).”
The influence of soil properties on the structure of bacterial and fungal communities across land-use types (2008, methodology): “Fungal sequences were aligned using MUSCLE 3.6 (Edgar, 2004) and compared to an in house database of 100 fungal 18S sequences derived from the AFTOL data set (Lutzoni et al., 2004) using the BLAST algorithm (Altschul et al., 1990) to determine taxonomic classification.”
A 567‐Taxon Data Set for Angiosperms: The Challenges Posed by Bayesian Analyses of Large Data Sets (2007, background): “Perhaps most notable are recent Bayesian analyses of fungi (Lutzoni et al. 2004), especially a two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla.”
Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota (2006, background): “The Basidiomycota is generally regarded as having three major clades (Swann and Taylor 1995; Lutzoni et al. 2004; Taylor et al. 2004; Matheny et al. 2007): the Agaricomycotina (= Hymenomycetes), the Ustilaginomycotina (= Ustilaginomycetes), and the Pucciniomycotina (= Urediniomycetes).”
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi (2014, methodology): “It was subsequently expanded to Fungi—initially using a divergent set of sequences generated by the collaborative Assembling the Fungal Tree of Life project (AFToL) (44).”
Fungal endophytes: diversity and functional roles. (2009, background): “Interestingly, numerous ascomycetous plant pathogens and saprotrophs are derived from these same lineages (Lutzoni et al., 2004; James et al., 2006).”