Ecological niche breadth and the mechanisms facilitating its evolution are fundamental to understanding adaptation to changing environments, persistence of generalist and specialist lineages and the formation of new species. Woody substrates are structurally complex resources utilized by organisms with specialized decay machinery. Wood-decaying fungi represent ideal model systems to study evolution of niche breadth, as they vary greatly in their host range and preferred decay stage of the substrate. In order to dissect the genetic basis for niche specialization in the invasive brown rot fungus Serpula lacrymans, we used phenotyping and integrative analysis of phylogenomic and transcriptomic data to compare this species to wild relatives in the Serpulaceae with a range of specialist to generalist decay strategies. Our results indicate specialist species have rewired regulatory networks active during wood decay towards decreased reliance on enzymatic machinery, and therefore nitrogen-intensive decay components. This shift was likely accompanied with adaptation to a narrow tree line habitat and switch to a pioneer decomposer strategy, both requiring rapid colonization of a nitrogen-limited substrate. Among substrate specialists with narrow niches, we also found evidence for pathways facilitating reversal to generalism, highlighting how evolution may move along different axes of niche space.

Data submission accompanying the article "Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans"

The data package is structured into three sections:

1) Functional annotation

    AnnotationDB.txt - Tab-delimited file containing all genes predicted, ID mapping,
                       eggNOG annotations, cluster IDs and GO annotations (merged from
                       eggNOG and InterProScan).
                       
                       
2) Phylogenomic Analysis

   gene_trees.zip - Gene trees (Newick format) for all clusters used for orthology
                       assignments and phylogenomic analysis.
                       
   alignments.zip - Alignments (FASTA format) used to build gene trees.
   
   OG_information.txt - Tab-delimted file containing orthogroup assignments. Information
                           includes orthogroup number, cluster number, gene IDs for each
                           strain and whether it's a one-to-one or one/many-to-many ortholog.
                           Note that for one-to-many and many-to-many orthologs the same gene
                           IDs may appear in several orthogroups.
                           
3) Genome Annotations

   Annotation files for each strain (zipped). Note that each locus may be associated with
   multiple proteins or transcripts if alternative splicing was predicted.
   
   Each compressed directory contains:

   *.gff - Gene annotations in GFF format
   *.proteins.fasta - Predicted proteins in FASTA format
   *.CDS.fasta - Coding sequence in FASTA format
   *.transcripts.fasta - Transcripts in FASTA format