Molecular phylogenetics of sessile Dolium sedentarium, a petalomonad euglenid

The euglenids are a species-rich group of flagellates with varying modes of nutrition that can be found in diverse habitats. Phagotrophic members of this group gave rise to phototrophs and hold the key to understanding the evolution of euglenids as a whole, including the evolution of complex morphological characters like the euglenid pellicle. Yet to understand the evolution of these characters, a comprehensive sampling of molecular data is needed to correlate morphological and molecular data and to estimate a basic phylogenetic backbone of the group. While the availability of SSU rDNA and, more recently, multigene data from phagotrophic euglenids has improved, several ‘orphan’ taxa remain without any molecular data whatsoever. Dolium sedentarium is one such taxon: It is a rarely-observed phagotrophic euglenid that inhabits tropical benthic environments and is one of the few known sessile euglenids. Based on morphological characters, it has been thought of as part of the earliest branch..., A single cell of Dolium sedentarium was collected from Spaanse Water mangrove in Curaçao in April 2022 (12.070621, -68.860269) via manual isolation with a micropipette, imaged on a Leica DLIM inverted microscope at 630x and a Sony a7RIII camera, and deposited in lysis buffer (see Picelli et al 2014). After 4 freeze-thaw cycles for lysis, a single-cell transcriptome was generated with the SmartSeq2 protocol (Picelli et al 2014), and sequenced on an Illumina MiSeq (2x250bp), multiplexed with other libraries.
Raw reads were read-corrected with rcorrector (version 1.0.4), adapter- and quality-trimmed with trimmomatic (version 0.39), and assembled with rnaSPAdes (version 3.15.1). Coding regions were determined with Transdecoder (version 5.5.0).
Additional assembly metrics shown in the multiQC report were generated with QUAST (version 5.0.2) and BUSCO (version 5.4.3).
SSU-rDNA sequences from the assembly were extracted with barrnap (version 0.9), and those sequences were blasted against GenBa..., Alignment-files in .fasta format can be opened with any text editor (e.g. SublimeText) or alignment viewers like AliView or SeaView.
Assemblies (.fasta and .pep) files can be opened with any text editor like SublimeText.
Tree-files in NEWICK-format (ending in .treefile or .tre) can be opened with a tree viewer like FigTree, Archaeopteryx, or iTOL EMBL.
The multiQC-report (ending in .html) can be opened with any browser.