Data from: Homospermidine synthase evolution and the origin(s) of pyrrolizidine alkaloids in Apocynaceae

Premise: Enzymes encoded by paralogous genes producing identical
specialized metabolites in distantly related plant lineages are strong
evidence of parallel phenotypic evolution. Inference of phenotypic
homology for metabolites produced by orthologous genes is less
straightforward, since orthologs may be recruited in parallel into novel
pathways. In prior research on pyrrolizidine alkaloids (PAs), specialized
metabolites of Apocynaceae, the evolution of homospermidine synthase
(HSS), an enzyme of PA biosynthesis, was reconstructed and a single origin
of PAs inferred because HSS enzymes of all known PA-producing
Apocynaceae species are orthologous and descended from an ancestral enzyme
with the motif (VXXXD) of an optimized HSS. The Methods: We increased
sampling, tested the effect of amino acid motif on HSS function, revisited
motif evolution, and tested for selection to infer evolution of HSS
function and its correlation with phenotype. Results: Some evidence
supports a single origin of PAs: an IXXXD HSS-like gene, similar in
function to VXXXD HSS, evolved in the shared ancestor of all PA-producing
species; loss of HSS function occurred multiple times via pseudogenization
and perhaps via evolution of an IXXXN motif. Other evidence indicates
multiple origins: the VXXXD motif, highly correlated with the PA
phenotype, evolved two or four times independently; the ancestral IXXXD
gene was not under positive selection, while some VXXXD genes were; and
substitutions at sites experiencing positive selection occurred on
multiple branches in the HSS-like gene tree. Conclusions: The complexity
of the genotype-function-phenotype map confounds the inference of PA
homology from HSS-like gene evolution in Apocynaceae.