@article {cho_genomic_2024,
	title = {Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses},
	journal = {PLOS Genetics},
	volume = {20},
	number = {4},
	year = {2024},
	note = {Publisher: Public Library of Science},
	pages = {e1011218},
	abstract = {Symbiomonas scintillans Guillou et Chr{\'e}tiennot-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 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.},
	keywords = {Eukaryota, Gene prediction, genomics, metagenomics, RCC24, RCC257, Shotgun sequencing, Transcriptome analysis, Viral genomics, Whole genome amplification},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1011218},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011218},
	author = {Cho, Anna and Lax, Gordon and Livingston, Samuel J. and Masukagami, Yumiko and Naumova, Mariia and Millar, Olivia and Husnik, Filip and Keeling, Patrick J.}
}
@article {cho_phylogenomic_2023,
	title = {Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean},
	journal = {Molecular Phylogenetics and Evolution},
	year = {2023},
	month = {nov},
	pages = {107964},
	abstract = {Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.},
	keywords = {benthic protists, Bigyra, MAST-6, phylogenomics, Placididea, RCC1078, RCC257, Stramenopile},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2023.107964},
	url = {https://www.sciencedirect.com/science/article/pii/S1055790323002646},
	author = {Cho, Anna and Tikhonenkov, Denis V. and Lax, Gordon and Prokina, Kristina I. and Keeling, Patrick J.}
}
