DOI: 10.5061/dryad.4f4qrfj93
title: Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans

description: 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.
description: 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,<br>                   
     eggNOG annotations, cluster IDs and GO annotations (merged
 from<br>                        eggNOG and InterProScan).<br>
                        <br>                        <br> 2)
 Phylogenomic Analysis    gene_trees.zip - Gene trees
 (Newick format) for all clusters used for orthology<br>          
              assignments and phylogenomic analysis.<br>          
              <br>    alignments.zip - Alignments (FASTA format) used
 to build gene trees.<br>    <br>    OG_information.txt -
 Tab-delimted file containing orthogroup assignments. Information<br>
                            includes orthogroup number, cluster number,
 gene IDs for each<br>                            strain and whether
 it's a one-to-one or one/many-to-many ortholog.<br>          
                  Note that for one-to-many and many-to-many orthologs the
 same gene<br>                            IDs may appear in several
 orthogroups.<br>                            <br> 3) Genome
 Annotations    Annotation files for each strain
 (zipped). Note that each locus may be associated with<br>   
 multiple proteins or transcripts if alternative splicing was
 predicted.<br>    <br>    Each compressed directory
 contains:    *.gff - Gene annotations in GFF
 format<br>    *.proteins.fasta - Predicted proteins in FASTA
 format<br>    *.CDS.fasta - Coding sequence in FASTA
 format<br>    *.transcripts.fasta - Transcripts in FASTA
 format<br>    <br>    <br>    <br>