The Bacterial Diversity Lurking in Protist Cell Cultures

Aponte, Ameris; Gyaltshen, Yangtsho; Burns, John A.; Heiss, Aaron A.; Kim, Eun-Soo; Warring, Sally D.

doi:10.1206/3975.1

Cited by 5 publications

(3 citation statements)

References 57 publications

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“…Notably, Marinobacter spp., Labrenzia spp., and Hyphomonas spp. were all reported to be common in cultures of Ostreoccocus tauri, Symbiodiniaceae, Alexandrium spp., and discobids [54][55][56][57][58][59][60]. Accounting for this overwhelming representation of culture-associated bacteria, a subset of whole-genome amplification (WGA) data was selected and reassembled based on lower GC content, which is usually associated with endosymbionts.…”

Section: No Bacterial Sequences From Known Clades Of Common Endosymbi...mentioning

confidence: 99%

Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses

Cho,

Lax,

Livingston

et al. 2024

PLoS Genet

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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 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.

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Section: No Bacterial Sequences From Known Clades Of Common Endosymbi...mentioning

confidence: 99%

Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses

Cho,

Lax,

Livingston

et al. 2024

PLoS Genet

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“…For the genomic dataset of M. sphyraenae , we first identified the main bacterial contaminants from the initial genome assemblies 51 . In addition, we established a customs database consisting of contigs assembled from Illumina sequencing data from bacteria only enrichment cultures derived from the lab’s several xenic protist cultures.…”

Section: Technical Validationmentioning

confidence: 99%

High quality genome and transcriptome data for two new species ofMantamonas, a deep-branching eukaryote clade

Blaz

Galindo

Heiss

et al. 2023

Preprint

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Mantamonads were long considered to represent an "orphan" lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the "CRuMs" supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.

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“…For the genomic dataset of M. sphyraenae , we first identified the main bacterial contaminants from the initial genome assemblies 53 . In addition, we established a custom database consisting of contigs assembled from Illumina sequencing data from bacteria only enrichment cultures derived from the lab’s several xenic protist cultures.…”

Section: Technical Validationmentioning

confidence: 99%

One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

Blaz,

Galindo,

Heiss

et al. 2023

Sci Data

Self Cite

View full text Add to dashboard Cite

Mantamonads were long considered to represent an “orphan” lineage in the tree of eukaryotes, likely branching near the most frequently assumed position for the root of eukaryotes. Recent phylogenomic analyses have placed them as part of the “CRuMs” supergroup, along with collodictyonids and rigifilids. This supergroup appears to branch at the base of Amorphea, making it of special importance for understanding the deep evolutionary history of eukaryotes. However, the lack of representative species and complete genomic data associated with them has hampered the investigation of their biology and evolution. Here, we isolated and described two new species of mantamonads, Mantamonas vickermani sp. nov. and Mantamonas sphyraenae sp. nov., for each of which we generated transcriptomic sequence data, as well as a high-quality genome for the latter. The estimated size of the M. sphyraenae genome is 25 Mb; our de novo assembly appears to be highly contiguous and complete with 9,416 predicted protein-coding genes. This near-chromosome-scale genome assembly is the first described for the CRuMs supergroup.

show abstract

The Bacterial Diversity Lurking in Protist Cell Cultures

Cited by 5 publications

References 57 publications

Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses

Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses

High quality genome and transcriptome data for two new species ofMantamonas, a deep-branching eukaryote clade

One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

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