Sam Kovaka’s Directed Study (BIOL 299) project last semester involved creation of a large phylogenomic tree using fungal genomes housed at the JGI MycoCosm portal. Sam implemented a pipeline that uses a set of gene clusters from 186 fungal genomes available on MycoCosm in mid-2013. The genes are aligned and concatenated, poorly aligned regions are removed with Gblocks, and the phylogeny is estimated with RAxML. The tree is then parsed into its component clades using least common ancestor statements. The strategy for parsing the tree is similar to that employed in the “mor” project that was developed in my lab way back in 2005, although that used only one gene, nuc-lsu rRNA. To read more about Sam’s project, visit the web site he created, or go straight to the tree below and then click on the terminals to open up the subclades (e.g., Agaricomycotina). I believe that this is the most complete genome-based fungal phylogeny currently available. Thanks to Igor Grigoriev, Bobby Otillar and Robert Riley at JGI for helping Sam (who is a second-year undergraduate in our lab) with this project.
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Hibbett lab news 