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..., For a majority of strains, cells grown in culture flasks were dislodged by scraping and collected by filtration over a 25mm 12 micron polycarbonate filter and flash frozen in liquid nitrogen. RNA was extracted using Machery Nagel plant RNA kit following manufacturers protocol except for cell lysis. This was carried out by bead beating for 5 minutes using a mixture of 0.1 and 0.5mm zirconia/silica beads (BioSpec) in a BioSpec Mini-Beadbeater. Sequencing libraries were constructed using the New England BioLabs Next Ultra RNA prep kit and sequenced on the Illumina HiSeq (4000) in paired-end mode (2×150bp) at either University of Maryland sequencing center or Genewiz (New Jersey, USA). Adapters and low-quality regions were removed using Trimmomatic. Trimmed reads were assembled using rnaSPAdes v3.13. In the case of O. luteus K-0444 and P. flagellatus RCC22, total RNA was extracted with TRI Reagent® (TR 118) (Molecular Research Center, Inc., Cincinnati, USA), following standard procedures. S..., , # Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics

[https://doi.org/10.5061/dryad.1g1jwsv5v](https://doi.org/10.5061/dryad.1g1jwsv5v)

**Description of the data and file structure**

Uploaded to this repository contains concatenated fasta or phylip files used to generate the phylogenies shown in the manuscript, genome scaffolds,  and all transcriptomic assemblies, ortholog selection, paralog selection, and alignments

### Files and variables

#### File: Ochro\_pseduo\_all.fas

**Description:** Fasta file of the Ochro dataset. This fasta file was used to construct Figure 1

#### File: Stram\_all.phy

**Description:** Phylip file of the stram dataset. This phylip file was used to construct  Figure S2

#### File: Picophagus\_genome\_scaffolds.fasta

**Description:** Fasta file of Picophagus genome scaffold contigs

#### File: 18S\_aligned.fasta

**Description:** 18S rRNA alignment of 259 ochrophyte sequences. 

#### File: 18S\_aligned\_tr...,