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

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopile, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to rest of the stramenopiles, but despite this their phylogenomic relationships remain poorly resolved. This is in part due to a number of missing lineages in phylogenomic analyses, and partly due to 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, 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 ochrophytes phylogenomic dataset, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signals or low phylogenetic biases. 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 robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with long internal branches or removing genes with highest level of phylogenetic noises recovered more topologies that were found in other phylogenomic analyses. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving a phylogenomic relationships, and removing the genes with high phylogenetic noises may aid in inferring more accurate phylogenomic relationships.