DOI: 10.5061/dryad.mw6m90644
title: Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but do reveal the presence of giant viruses

description: Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4
 μm) heterotrophic microbial eukaryote. The genus was named based
 on the presence of endosymbiotic bacteria in its endoplasmic
 reticulum, however, like most such endosymbionts neither the
 identity nor functional association with its host were known. We
 generated both amplification-free shotgun metagenomics and whole
 genome amplification sequencing data from S. scintillans strains
 RCC257 and RCC24, but were unable to detect any sequences from known
 lineages of endosymbiotic bacteria. The absence of endobacteria was
 further verified with FISH analyses. Instead, numerous contigs in
 assemblies from both RCC24 and RCC257 were closely related to
 prasinoviruses infecting the green algae Ostreococcus lucimarinus,
 Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV,
 respectively). Using the BpV genome as a reference, we assembled a
 near-complete 190 kbp draft genome encoding all hallmark prasinovirus
 genes, as well as two additional incomplete assemblies of closely related
 but distinct viruses from RCC247, and three similar draft viral genomes
 from RCC24, which we collectively call SsVs. A multi-gene tree showed the
 three SsV genome types branched within highly supported clades with each
 of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission
 electron microscopy also revealed a 190 nm virus-like particle similar to
 the morphology and size of the endosymbiont originally reported in S.
 scintillans. Overall, we conclude that S. scintillans currently
 does not harbour an endosymbiotic bacterium, but is
 associated with giant viruses.
description: Two strains of <em>Symbiomonas scintillans</em> were
 used to generate short-read Illumina NextSeq whole-genome amplified (WGA)
 sequencing data. The cells are individually isolated (50-100) for this.
 Viral contigs were identified and draft viral metagenomically assembled
 genomes (vMAGs) were generated using RagTag and annotated with
 Prokka.  Three vMAGs were obtained from each of the
 strains RCC24 and RCC257. Only the most complete vMAGs (i.e., BpV2-vMAGs)
 were annotated. Additionally, 22-core genes of
 prasinoviruses were searched in the WGA data to generate a multi-gene
 phylogeny. The identified genes were aligned with a previously compiled
 22-core gene dataset and trimmed. After verifying each of the genes using
 22 single-gene trees, the alignments were concatenated and used to
 construct multi-gene phylogenetic trees.
description: # Genomic analyses of *Symbiomonas scintillans* show no evidence for
 endosymbiotic bacteria but do reveal the presence of giant viruses
 [https://doi.org/10.5061/dryad.mw6m90644](https://doi.org/10.5061/dryad.mw6m90644) Genome and protein sequences of each of the three draft vMAGs from RCC24 and RCC257. The protein sequences were predicted with Prodiga-gv (Hyatt et al., 2010) and annotated with Prokka. ## Description of the data and file structure Genome (*.fasta), protein (*.faa), and annotation (.*gbk) information* and sequences are organized by the strain names. These files represent the contents of Figure 3, part of Table S2, and Figure S5. For the 22-gene tree, alignment files (*.mafft*), single-gene tree files (*iqtree*), trimmed files (*.trimal*), and concatenated files (*.concat*) include genes from both strain RCC24 and RCC257. Concatenation was done separately to include genes from RCC257 and genes from both RCC24 and RCC257. These files represent the contents of Figure 2 and Figure S4. ## Sharing/Access information Data was derived from the following sources: * The 22-core gene alignments of praisnoviruses used to search within our dataset were obtained from Bachy et al. (2021): 10.1038/s41396-021-00989-9. For additional queries, please contact the corresponding author at: [annacho.apteno@gmail.com](mailto:annacho.apteno@gmail.com) or [acho@mail.ubc.ca](mailto:acho@mail.ubc.ca)