Assembling the Fungal Tree of Life: constructing the Structural and Biochemical Database

Abstract

A major goal of the Assembling the Fungal Tree of Life project is to create a searchable database <http://aftol.umn.edu> of selected ultrastructural and biochemical characters from published and new data for use in phylogenetic and other analyses. While developing this database such issues as evaluating specimen fixation quality in published micrographs, organizing data to accommodate characters that were dependent on location and developmental stage, and requiring accountability of data contributors were addressed. Character states for three traits, septal pore apparatus, nuclear division and spindle pole body cycle, are illustrated, and character states are resolved with maximum parsimony and plotted on a summary cladogram of known phylogenetic relationships of the Fungi. The analysis illustrates the inherent phylogenetic signal of these characters, the paucity of comparable characters and character states in subcellular studies and the challenges in establishing a comprehensive structural and biochemical database of the Fungi.

Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient

“…These sequences matched to bacteria in the phylum Proteobacteria (65), Actinobacteria (27) and the Bacteroidetes, Firmicutes, and Planctomyces (16 combined). Based on linear regression, we found a significant positive correlation between the proportion active bacterial OTUs and the relative abundance of rpfC genes (F 1,5 =9.68, R 2 =0.59, p=0.03).…”

“…Raw environmental sequences generated for this study can be accessed in the MG-RAST database [25] To generate phylogenies from the environmental sequences, we placed representative OTU sequences onto reference phylogenies. For the bacteria, we used an existing phylogeny from Kembel et al (2012) [26], and for the fungi, we built the reference using 952 non-redundant full-length LSU sequences from the Assembling the Fungal Tree of Life project [27] downloaded from GenBank (NCBI). Filtered fungal and bacterial OTU sequences were placed onto their respective reference trees using pplacer [28].…”

The Fungi: 1, 2, 3 … 5.1 million species?

“…Additional pages were contributed to the Tree of Life web project (http://www.tolweb.org/Fungi/2377) to make information on fungi more accessible to students and the general public. Two objectives of the ongoing AFTOL-2 project include increased taxon sampling of fungi for molecular data and the discovery of correlated morphological and biochemical characters (AFTOL Structural and Biochemical Database, https://aftol.umn.edu;Celio et al, 2006 ). ( Kirk et al, 2008 ) reported 97 330 species of described fungi at the " numbers of fungi " entry.…”

Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

“…The Assembling the Fungal Tree of Life (AFTOL) project set up yet another valuable online resource for fungi, data matrices, and phylogenetic reconstructions (29). The data elements are curated from published literature and include post-taxonomic assessments for inclusion in the AFTOL database, combining character illustrations and molecular data.…”