Data from: Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics

Ochrophyta is a vast and morphologically diverse group of algae with
complex plastids, including familiar taxa with fundamental ecological
importance (diatoms or kelp), and a wealth of lesser-known and obscure
organisms. The sheer diversity of ochrophytes poses a challenge for
reconstructing their phylogeny, with major gaps in sampling and an
unsettled placement of particular taxa yet to be tackled. We sequenced
transcriptomes from 25 strategically selected representatives and used
these data to build the most taxonomically comprehensive
ochrophyte-centered phylogenomic supermatrix to date. We employed a
combination of approaches to reconstruct and critically evaluate the
relationships among ochrophytes. While generally congruent with previous
analyses, the updated ochrophyte phylogenomic tree resolved the position
of several taxa with previously uncertain placement, and supported a
redefinition of the classes Picophagea and Synchromophyceae. Our results
indicated that the heterotrophic plastid-lacking heliozoan Actinophrys sol
is not a sister lineage of ochrophytes, as proposed recently, but rather
phylogenetically nested among them, implying that it lacks a plastid due
to loss. In addition, we found the heterotrophic ochrophyte Picophagus
flagellatus to lack all hallmark plastid genes, yet to exhibit
mitochondrial proteins that seem to be genetic footprints of a lost
plastid organelle. We thus document, for the first time, plastid loss in
two separate ochrophyte lineages. Furthermore, by exploring eDNA data we
enrich the ochrophyte phylogenetic tree by identifying five novel
uncultured class-level lineages. Altogether, our study provides a new
framework for reconstructing trait evolution in ochrophytes and
demonstrates that plastid loss is more common than previously thought.