Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene..., Nine cultures of under-represented ochrophytes (including Olisthodiscophyceae, Schizocladiophyceae, Picophagea, and Phaeothamniophyceae) were obtained from various culture collections, in addition to manually isolated Vicicitus globosus from environmental samples. Except for V. globosus, we extracted RNA using TRIzol or CTAB. RNA extracts (and single-cell isolates of V. globosus) were then subject to poly-A selection-based Smart-Seq2 protocol cDNA synthesis. The sequencing libraries were prepared using Illumina Flex Library Preparation Kit followed by Illumina NextSeq (150bp paired-end) mid-output transcriptomic sequencing. 
Filtered and processed transcriptomes were then used to look for orthologs archived in PhyloFisher v1.1.2 (https://github.com/TheBrownLab/PhyloFisher) which were then used to concatenate the main supermatrix ('231-supermatrix'). 
Using various gene properties calculated from the '231-supermatrix' using R-scripts posted on https://github.com/mongiardino/genesortR, we..., , # Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages

[https://doi.org/10.5061/dryad.f4qrfj73q](https://doi.org/10.5061/dryad.f4qrfj73q)

Supplementary tree files, supermatrices, and calculated gene properties generated from different gene-filtering criteria are described below.

## Description of different gene-filtering criteria

Genes were selected from a 241-gene-set based on different gene filtering criteria described below. The resulting genes were then used to concatenate supermatrices that were then used to reconstruct phylogenomic trees. Therefore, each of the supermatrices and treefiles were labelled based on gene-filtering criteria and their size parameters (e.g., A100 indicates genes selected based on A-criteria with top 100 values; S180 indicates genes selected based on S criteria with top 180 highest values). 

(A) high values of treeness and occupancy
(B) high values of average_bootstrap(BS)_support, Robinson-Foulds similarity (rob...