MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities

Guyomar, Cervin; Delage, Wesley; Legeai, Fabrice; Mougel, Christophe; Simon, Jean‐Christophe; Lemaitre, Claire

doi:10.1101/2019.12.13.875021

Cited by 4 publications

(5 citation statements)

References 27 publications

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“…Being a host-based approach to endosymbiont discovery, the "next-generation taxonomy" approach is applicable to known symbiotic communities. Software (MinYS) has also recently been reported to specifically identify symbionts from genome assemblies of symbiotic communities by using reference genomes (Guyomar et al, 2020). Although genetic code 4 (UGA stop codons recoded to tryptophan) has been reported to only occur rarely (Yamao et al, 1985;Knight et al, 2001;McCutcheon et al, 2009), our findings raise the enticing prospect that searching contigs and MAGs for this recoding may reveal new symbionts, including members of the verrucomicrobial "Nucleococcus cluster" (Figure 1).…”

Section: Discussionmentioning

confidence: 73%

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

et al. 2021

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Organic Lake in Antarctica is a marine-derived, cold (−13∘C), stratified (oxic-anoxic), hypersaline (>200 gl–1) system with unusual chemistry (very high levels of dimethylsulfide) that supports the growth of phylogenetically and metabolically diverse microorganisms. Symbionts are not well characterized in Antarctica. However, unicellular eukaryotes are often present in Antarctic lakes and theoretically could harbor endosymbionts. Here, we describe Candidatus Organicella extenuata, a member of the Verrucomicrobia with a highly reduced genome, recovered as a metagenome-assembled genome with genetic code 4 (UGA-to-Trp recoding) from Organic Lake. It is closely related to Candidatus Pinguicocccus supinus (163,218 bp, 205 genes), a newly described cytoplasmic endosymbiont of the freshwater ciliate Euplotes vanleeuwenhoeki (Serra et al., 2020). At 158,228 bp (encoding 194 genes), the genome of Ca. Organicella extenuata is among the smallest known bacterial genomes and similar to the genome of Ca. Pinguicoccus supinus (163,218 bp, 205 genes). Ca. Organicella extenuata retains a capacity for replication, transcription, translation, and protein-folding while lacking any capacity for the biosynthesis of amino acids or vitamins. Notably, the endosymbiont retains a capacity for fatty acid synthesis (type II) and iron–sulfur (Fe-S) cluster assembly. Metagenomic analysis of 150 new metagenomes from Organic Lake and more than 70 other Antarctic aquatic locations revealed a strong correlation in abundance between Ca. Organicella extenuata and a novel ciliate of the genus Euplotes. Like Ca. Pinguicoccus supinus, we infer that Ca. Organicella extenuata is an endosymbiont of Euplotes and hypothesize that both Ca. Organicella extenuata and Ca. Pinguicocccus supinus provide fatty acids and Fe-S clusters to their Euplotes host as the foundation of a mutualistic symbiosis. The discovery of Ca. Organicella extenuata as possessing genetic code 4 illustrates that in addition to identifying endosymbionts by sequencing known symbiotic communities and searching metagenome data using reference endosymbiont genomes, the potential exists to identify novel endosymbionts by searching for unusual coding parameters.

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Section: Discussionmentioning

confidence: 73%

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

et al. 2021

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“…It may be that the genomes of these bacterial species are more difficult to assemble (e.g., higher content of repetitive regions), and thus, were discarded along the assembly pipeline because they did not meet the completeness/contamination parameters. Further studies using targeted approaches (e.g., MinYS [65]) are needed to evaluate their potential role as an endosymbiont of bird's nasal mites. Lastly, we also found species from bacterial genera known to contain species that can cause zoonoses, like Escherichia, Nocardia, and Salmonella [66].…”

Section: Discussionmentioning

confidence: 99%

Genome-resolved metagenomic analyses reveal the presence of a bacterial endosymbiont in an avian nasal mite (Rhinonyssidae; Mesostigmata)

Osuna‐Mascaró

Doña

Johnson

et al. 2021

Preprint

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Rhinonyssidae (Mesostigmata) is a family of nasal mites only found in birds. All species are hematophagous endoparasites, which may damage the nasal cavities of birds, and also could be potential reservoirs or vectors of other infections. However, the role of members of Rhinonyssidae as disease vectors in wild bird populations remains uninvestigated, with studies of the microbiomes of Rhinonyssidae being almost non-existent. In the nasal mite (Tinaminyssus melloi) from rock doves (Columba livia), a previous study found evidence of a highly abundant putatively endosymbiotic bacteria from Class Alphaproteobacteria. Here, we expanded the sample size of this species, incorporated contamination controls, and increased sequencing depth in shotgun sequencing and genome-resolved metagenomic analyses. Our goal was to increase the information regarding this mite species with its putative endosymbiont. Our results support the endosymbiotic nature of this bacterial taxon, which is the first described for bird’s nasal mites to date, and improve the overall understanding of the microbiota inhabiting these mites.

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“…With the raw sequencing data, we used the MinYS pipeline (Guyomar et al, 2020) to assemble Blochmannia genomes for each sample. MinYS used samples mixed with host and bacterial DNA in a pipeline that allows targeted assembly of bacterial genomes.…”

Section: Methodsmentioning

confidence: 99%

“…With the raw sequencing data, we used the MinYS pipeline (Guyomar et al, 2020) to assemble Blochmannia genomes for each sample.…”

Section: Blochmannia Genome Assemblies and Annotationmentioning

confidence: 99%

Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genusCamponotus) and theirBlochmanniaendosymbionts

Manthey

Girón

Hruska

2022

Ecology and Evolution

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Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole‐genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex ) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole‐genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome‐wide estimates of genetic drift and number of genes with relaxed selection pressures.

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MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities

Cited by 4 publications

References 27 publications

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake

Genome-resolved metagenomic analyses reveal the presence of a bacterial endosymbiont in an avian nasal mite (Rhinonyssidae; Mesostigmata)

Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genusCamponotus) and theirBlochmanniaendosymbionts

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