L constructs orthologous groups of proteins across multiple eukaryotic species using a Markov Cluster algorithm

L constructs orthologous groups of proteins across multiple eukaryotic species using a Markov Cluster algorithm to group orthologs and paralogs. Proteins not grouped into any orthologous group were identified as singletons and designated as unique to their respective genomes. When an orthologous group was identified in which all proteins were derived the same species, we considered this to be a paralogous group, and all proteins in that group were designated as unique to that species.Fungal genome sequence availabilityThe genome sequences and annotations for the 4 fungi in this study are available at the JGI fungal genomics resource MycoCosm [56] at http://genome.jgi.doe.gov/programs/fungi/index.jsf;PLOS ONE | DOI:10.1371/journal.pone.0157844 July 19,6 /Secretome Profiles of Mn(II)-Oxidizing Fungigenomes are identified in MycoCosm as Altal1 (A. alternata), Parsp1 (P. sporulosum), Pyrsp1 (Pyrenochaeta sp.), and Stasp1 (Stagonospora sp.). Genome assemblies and annotations were also deposited at DDBJ/ENA/GenBank under the following PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21184822 accession numbers: LXPP00000000 (A. alternata), LXPO00000000 (P. sporulosum), LXSZ00000000 (Pyrenochaeta sp.), and LXTA000 00000 (Stagonospora sp.). The versions described in this paper are LXPP01000000, LXPO010 00000, LXSZ01000000, and LXTA01000000, respectively.ResultsA complete list of the proteins experimentally identified in each of the four fungal secretomes, including assigned functions and CAZy and MEROPS classifications (for carbohydrate-active enzymes and peptidases, respectively), is presented in S1 Table. Complete lists of proteins in the genome-based predicted secretomes of each fungus are presented in S2 5 MedChemExpress Metacept-3 Tables. For the purposes of this manuscript, experimental secretome composition was evaluated for each fungus across the entire 21-day study. In other words, proteins were included if they were identified in secretomes harvested at any of the 3 time points (7, 14, or 21 days) to allow for comparison of the full suite of secretome proteins. In general, the diversity of proteins in each fungal secretome varied less than 6 across each time point and no more than 10 in any one protein functional group over the 21-day study. Thus, the suite of proteins identified in each secretome was fairly consistent over time. A detailed analysis of the temporal changes in the abundance of these proteins will be presented in a separate publication.Secretome sizeOver 1,300 proteins were identified in the experimental secretome of each of the 4 fungi, ranging from 1,368 identified proteins in the Pyrenochaeta sp. secretome to 1,617 identified proteins in the Stagonospora sp. secretome (Fig 1A). Within CAZy and MEROPS classifications, between 518 (in the Pyrenochaeta sp. secretome) and 576 (in the Stagonospora sp. secretome) enzymes were identified. When the experimental secretomes were filtered to only include those identified proteins that are predicted to be secreted based on genomic analysis, the secretome size was reduced to <700 identified proteins for each species (Fig 1B), including 365 (in the P. sporulosum secretome) to 412 (in the Stagonospora sp. secretome) identified proteins that were classified within CAZy and MEROPS functional groups. The size of the full predicted secretomes (i.e., based on genomic data only) of each fungus was comparable to that of the experimental secretomes, ranging from 1,352 proteins in the A. alternata predicted secretome to 1,604 proteins in the P. sporulosum predicted secret.