Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities

Widen, Sonya A.; Bes, Israel Campo; Koreshova, Alevtina; Krogull, Daniel; Burga, Alejandro

doi:10.1101/2022.07.12.499685

Cited by 11 publications

(11 citation statements)

References 94 publications

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“…3A). Alternatively, LGT mediated by viruses could explain how genes are transferred between eukaryotes ( 47 ). Independent of the precise route for LGT across eukaryotes, our study provides evidence for rampant LGT of gene homologs within the animal kingdom and suggests that the acquisition of C 24 -SMTs provides animals with a strong selective advantage.…”

Section: The Complex Evolutionary History Of C24-smtsmentioning

confidence: 99%

De novo phytosterol synthesis in animals

Michellod

Bien

Birgel

et al. 2023

Science

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Sterols are vital for nearly all eukaryotes. Their distribution differs in plants and animals, with phytosterols commonly found in plants whereas most animals are dominated by cholesterol. We show that sitosterol, a common sterol of plants, is the most abundant sterol in gutless marine annelids. Using multiomics, metabolite imaging, heterologous gene expression, and enzyme assays, we show that these animals synthesize sitosterol de novo using a noncanonical C-24 sterol methyltransferase (C 24 -SMT). This enzyme is essential for sitosterol synthesis in plants, but not known from most bilaterian animals. Our phylogenetic analyses revealed that C 24 -SMTs are present in representatives of at least five animal phyla, indicating that the synthesis of sterols common to plants is more widespread in animals than currently known.

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Section: The Complex Evolutionary History Of C24-smtsmentioning

confidence: 99%

De novo phytosterol synthesis in animals

Michellod

Bien

Birgel

et al. 2023

Science

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“…These scenarios are not mutually exclusive - it is possible that polintoviruses have both life-strategies that include within genome propagation and free particle production. A recent study also supports this possibility where it was shown that polintoviruses have horizontally transferred key genes across nematode lineages through a mechanism that requires free virus production 67 .…”

Section: Resultsmentioning

confidence: 81%

“…Recent studies have started to illuminate the accessory gene functions and factors shaping the genomic landscape of polintoviruses. Of note is a recent report on polintoviruses in nematodes, where these elements were found to be a vector of horizontal transfer of key nematode protease and kinase genes 67 . Specifically, polintoviruses took up these genes as cargoes and transferred them between different nematode species on a global scale.…”

Section: Functional Profile Of the Stony Coral Polintovirusesmentioning

confidence: 99%

Widespread Occurrence and Diverse Origins of Polintoviruses Influence Lineage-specific Genome Dynamics in Stony Corals

Stephens,

Faghihi,

Moniruzzaman

2023

Preprint

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Stony corals (OrderScleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for ‘endogenous’ viruses. Our study uncovered a remarkable number of integrated viral elements recognized as ‘Polintoviruses’ (ClassPolintoviricetes) in 30Scleractiniagenomes, with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony corals, alongside presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, followed by their paralogous expansions shaped stony coral genomes. Gene expression analysis reveals all polintovirus structural and non-structural hallmark genes are expressed, strongly supporting free virion production from polintoviruses. Our results revealing a significant polintovirus diversity across theScleractiniaorder open a new research avenue into their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.

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“…Our analyses across 1,237 fungal genomes revealed an uneven distribution of potential host-TE fusions among major fungal phylogenies, with a higher percentage of genes involved in host-TE fusions in Saccharomycotina. Opposed to vertebrates, plants and nematodes, where terminal inverted repeat transposase domains are predominantly associated with host-TE fusions, we detected helicases as the most abundant TE-derived domains [20,27,34]. The host domains of host-TE fusions show a broader diversity in function, but tend to be associated with processes involved in genome integrity and defense against foreign sequences including TEs.…”

Section: Discussionmentioning

confidence: 99%

A systematic screen for co-option of transposable elements across the fungal kingdom

Oggenfuss,

Badet,

Croll

2023

Preprint

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How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1,237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived fromAcadem,KolobokorHelitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of how domains likely derived from TEs contribute to the evolution of protein functions.

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Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities

Cited by 11 publications

References 94 publications

De novo phytosterol synthesis in animals

De novo phytosterol synthesis in animals

Widespread Occurrence and Diverse Origins of Polintoviruses Influence Lineage-specific Genome Dynamics in Stony Corals

A systematic screen for co-option of transposable elements across the fungal kingdom

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