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
filtering criteria to identify the most phylogenetically informative
genes. We generated ten new transcriptomes from various culture
collections and single-cell isolation from an environmental sample, added
these to an existing phylogenomic dataset, and examined the effects of
selecting genes with high phylogenetic signal or low phylogenetic noise.
For some previously contentious relationships, we find a variety of
analyses and gene filtering criteria consistently unite previously
unstable grouping with strong statistical support. For example, we
recovered a robust grouping of Eustigmatophyceae with
Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed
a sister lineage to Pinguiophyceae. Selecting genes with high phylogenetic
signal or data quality recovered more stable topologies. Overall, we find
that adding under-represented groups across different lineages is still
crucial in resolving phylogenomic relationships, and discrete gene
properties affect lineages of stramenopiles differently which may be
further explored to better understand the molecular evolution of
stramenopiles.