Browsing by Author "Kauff, F."
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- Assembling the fungal tree of life: progress, classification, and evolution of subcellular traitsPublication . Lutzoni, F.; Kauff, F.; Cox, C. J.; McLaughlin, D.; Celio, G.; Dentinger, C.; Padamsee, M.; Hibbett, D. S.; James, T. Y.; Baloch, E.; Grube, M.; Reeb, V.; Hofstetter, V.; Schoch, C. L.; Arnold, A. E.; Miadlikowska, J.; Spatafora, J.; Johnson, D.; Hambleton, S.; Crockett, M.; Shoemaker, R.; Sung, G. -H.; Lücking, R.; Lumbsch, H. T.; O'Donnell, K.; Binder, M.; Diederich, P.; Ertz, D.; Gueidan, C.; Hansen, K.; Harris, R. C.; Hosaka, K.; Lim, Y. -W.; Matheny, P. B.; Nishida, H.; Pfister, D.; Rogers, J.; Rossman, A.; Schmitt, I.; Sipman, H.; Stone, J.; Sugiyama, J.; Yahr, R.; Vilgalys, R.Based on an overview of progress in molecular systematics of the true fungi(Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project ‘‘Assembling the Fungal Tree of Life’’ (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.
- Biopython: freely available Python tools for computational molecular biology and bioinformaticsPublication . Cock, P. J. A.; Antao, T.; Chang, J. T.; Chapman, B. A.; Cox, C. J.; Dalke, A.; Friedberg, I.; Hamelryck, T.; Kauff, F.; Wilczynski, B.; De Hoon, M. J. L.Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.
- Reconstructing the early evolution of Fungi using a six-gene phylogenyPublication . James, T. Y.; Kauff, F.; Schoch, C. L.; Matheny, P. B.; Hofstetter, V.; Cox, C. J.; Celio, G.; Gueidan, C.; Fraker, E.; Miadlikowska, J.; Lumbsch, H. T.; Rauhut, A.; Reeb, V.; Arnold, A. E.; Amtoft, A.; Stajich, J. E.; Hosaka, K.; Sung, G. -H.; Johnson, D.; O'Rourke, B.; Crockett, M.; Binder, M.; Curtis, J. M.; Slot, J. C.; Wang, Z.; Wilson, A. W.; Schüßler, A.; Longcore, J. E.; O'Donnell, K.; Mozley-Standridge, S.; Porter, D.; Letcher, P. M.; Powell, M. J.; Taylor, J. W.; White, M. M.; Griffith, G. W.; Davies, D. R.; Humber, R. A.; Morton, J. B.; Sugiyama, J.; Rossman, A.; Rogers, J.; Pfister, D.; Hewitt, D.; Hansen, K.; Hambleton, S.; Kohlmeyer, J.; Volkmann-Kohlmeyer, B.; Spotts, R. A.; Serdani, M.; Crous, P. W.; Hughes, K. W.; Matsuura, K.; Langer, E.; Langer, G.; Untereiner, W. A.; Lucking, R.; Budel, B.; Geiser, D. M.; Aptroot, A.; Diederich, P.; Schmitt, I.; Schultz, M.; Yahr, R.; Hibbett, D. S.; Lutzoni, F.; McLaughlin, D.; Spatafora, J.; Vilgalys, R.The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species.Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
- WASABI: an automated sequence processing system for multigene phylogeniesPublication . Kauff, F.; Cox, C. J.; Lutzoni, F.WASABI (Web Accessible Sequence Analysis for Biological Inference) is a software that provides the computational infrastructure for multiuser multigene phylogenetic projects.