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De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Figure 9

Phylogenetic analysis of the predicted phenylalanine ammonia lyase (PAL) proteins from eight fungi.

Numbers at branches indicate bootstrap support (10,000 bootstrap replications) in % for the neighbor joining tree, and clade credibilities for the Bayesian tree. Classes given on the right correspond to the taxonomy used by Liu and Hall [171], and in the NCBI Entrez Taxonomy Database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy). Sordariomycete proteins are given in blue with the exception of the S. macrospora protein SMAC_01196 that clusters with the Leotiomycete/Dothideomycete group and is given in red. Sequences for P. anserina were obtained from the Podospora anserina genome project (http://podospora.igmors.u-psud.fr/index.html) and for all other fungi from the Fungal Genome Initiative of the Broad Institute at (http://www.broad.mit.edu/ annotation/fungi/fgi/index.html). AN: Aspergillus nidulans, BC: Botrytis cinerea, CC: Coprinus cinereus (outgroup), CH: Chaetomium globosum, NC: Neurospora crassa, SM: Sordaria macrospora, PA: Podospora anserina, SN: Stagonospora nodorum (Phaeosphaeria nodorum).

Figure 9

doi: https://doi.org/10.1371/journal.pgen.1000891.g009