Reconstructing the early evolution of Fungi using a six-gene phylogeny

By Timothy Y. James, Frank Kauff, C. Schoch, P. B. Matheny, Valérie Hofstetter, C. Cox, G. Celio, C. Gueidan, E. Fraker, J. Miadlikowska and 60 more. Nature, 2006

1,796 citations recorded by the source corpus.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/185458f908ccf9f23e4308506aee2ffc4a129687

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Citations in the corpus

How many fungi make sclerotia (2015, background): “Two fun- gal phyla, Basidiomycota and Ascomycota, comprise the subkingdom Dikarya, a diverse group with ca. 100,000 described species (James et al., 2006).”
Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry (2015, methodology): “Eight eukaryotic outgroup species were included from James et al. (2006).”
Scraping the bottom of the barrel: are rare high throughput sequences artifacts? (2015, methodology): “LSU libraries were aligned against a modified James et al. (2006) reference (Brown et al., 2014), and gaps removed prior to downstream analyses.”
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi (2012, background): “Some also contributed sequences from regions of two additional optional genes, namely the second largest subunit of RNA polymerase II (RPB2; also an AFToL marker) (39) and a gene encoding aminichromosomemaintenance protein (MCM7), which were chosen based on their usefulness in phylogenetic studies a”
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification (2008, methodology): “Hidden Markov Models (HMMs) of the fl anking nuclear small sub-unit (nSSU), 5.8S, and nuclear large sub-unit (nLSU) were constructed from the large-scope fungal alignments of Tehler et al. (2003); Larsson et al. (2004); Binder et al. (2005); and James et al. (2006) using HMMER 2.3.2 (Eddy, 1998).”
Global emergence of Batrachochytrium dendrobatidis and amphibian chytridiomycosis in space, time, and host. (2009, background): “These fungi are characteristically aquatic and unique from other fungi in that they have a motile, flagellate zoospore (52).”
Microsporidia: a journey through radical taxonomical revisions (2009, background): “Other zygomycete lineages and Rozella are obviously candidates of interest.”
Incorporating molecular data in fungal systematics: a guide for aspiring researchers (2013, background): “7 one unlinked gene/marker in phylogenetic endeavours (James et al. 2006).”
Refined families of Sordariomycetes (2020, methodology): “This began with the AFTOL project which provided molecular data for the main orders and families of Ascomycota (James et al. 2006).”
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.”