Dataset contains supplementary data for 2014 article on phylogenomic "roadmap" for non-reducing polyketide synthases. It contains/references the original version of dataset.
Updated/expanded versions of the analysis will be linked below, when available.
21/09/2015: added the results of comparison of DTL-RANGER results with ALE results (both amalgamated and original topologies were compared, results on original BI consensus were benchmarked on 352 bipartitions shared with the amalgamated tree
15/08/2015: corrected badly linked PDF version of the reconciled gene tree in Downloads section - link pointed to reference NR-PKS listing instead
The species history is based on 149 fungal genomes (Caenorhabditis elegans was used as an outgroup). A curated alignment of 21 single-copy orthologs (chosen based on FUNYBASE recommendations)
was used to ascertain the phylogeny. Relaxed, log-normal autocorrelated clock with soft bounds under a birth death prior was used to calibrate the tree and obtain the chronogram.
A set of KS-AT modules extracted from 413 non-reducing PKS genes was used to construct the gene tree. Reconciliation data is based on ALE v0.3 and DTL-RANGER (with sampling multiple optimal reconciliations at random).
species tree infographic (with numbered nodes), additional tree infographic containing BI/ML supports
gene tree infographic with annotated events* and available functional annotations
* - individual reports on reconciliation/evolutionary events inferred by ALE are available after clicking on gene node numbers (e.g. g766) on the gene tree graphic
- Species tree data:
- concatenated alignment of orthologs: PHYLIP
- partition file: NEXUS
- Bayesian Inference species tree (callibrated chronogram, taxon numbers by NCBI/Taxonomy): Newick
- Maximum Likelihood species tree (taxon numbers by NCBI/Taxonomy): Newick
- list of species/model genomes: PDF
- list of single-copy orthologs: PDF
- dating constraints used: PDF
- rendering of Bayesian Inference species tree topology: PDF
- rendering of Maximum Likelihood species tree topology: PDF
- Gene tree data:
- final alignment of 414 KS-AT modules (including FUM1 HR-PKS outgroup): PHYLIP
- Bayesian Inference gene tree (w/o FUM1 outgroup):Newick
- Bayesian Inference gene tree, post-ALE reconciliation (no supports): Newick
- Reference NR-PKSs of known activity/end products: PDF
- rendering of gene tree (post-ALE reconciliation), with annotated gene structure and domain architecture: PDF
- Other supplementary data:
- mapping of sequence identifiers to gene names: CSV(Excel)
NOTE: positive identifiers correspond to NCBI/GenBank GIs, negative identifiers are from the internal database (with sequences from Ensembl/JGI/individual published genomes)
- splicing sites significantly associated with monophyletic clades (post-mapping to domain structure): PDF
- CHGs (Candidate Homolog Groups) elucidated with MCL: FASTA
- concordance of DTL-RANGER results with ALE predictions (note: statistics for the original BI consensus tree are based on 352 shared bipartitions): PDF