Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs

Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly-studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes (SAGs), and only a single formal described species, Eupelagonema oceanica. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we c..., Two single cells of eupelagonemids were isolated from seawater that was collected with a Niskin bottle from 300m depth at station KSC10 (Lat. 51.6505, Lon. -127.9516; Calvert Island, British Columbia, Canada) on July 3rd 2022. The cells were manually isolated from the concentrated seawater with a microcapillary and imaged on a Leica DMIL-LED inverted microscope equipped with a Sony alpha7S III camera at 630X magnification.
The isolated cells were rinsed three times in drops of clean seawater and dispensed into 2µl of Smart-seq3 lysis buffer. cDNA was generated using Smart-seq3 with 24 PCR-cycles for cDNA amplification, libraries were prepared with Illumina DNA library prep and sequenced on an Illumina NextSeq 500 platform with 2x150bp paired-end reads.
Raw reads were read-corrected with rcorrector version 1.0.5, adapter- and quality-trimmed with trimmomatic version 0.39 using parameters ILLUMINACLIP: 2:30:10 LEADING:5 SLIDINGWINDOW:5:16 MINLEN:60, with the following sequences trimmed: T..., , # Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs

[https://doi.org/10.5061/dryad.hqbzkh1pj](https://doi.org/10.5061/dryad.hqbzkh1pj)

These are supplemental data for the publication \"Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs\", in The ISME Journal [https://doi.org/10.1093/ismejo/wrae040](https://doi.org/10.1093/ismejo/wrae040).

It contains the assembled single-cell transcriptomes of cells \"Eupelagonemid 7\" and \"Eupelagonemid 8\", two cells of eupelagonemids isolated from the deep pelagic ocean that were placed in a multigene phylogeny, resolving their position among diplonemids. This dataset also contains the SSU rRNA gene alignment and subsequent tree data, and all multigene data used to construct the final phylogenomic tree.

## Description of the data and file structure

There are 4 main parts to this dataset:

1. Raw micrograph images of Eupelagonemid 7 and Eupelagonemid 8. In TIFF-format (can be open...