Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity

Author:

Gluck-Thaler Emile123ORCID,Vogan Aaron A4ORCID

Affiliation:

1. Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel , Neuchâtel , Neuchâtel 2000 , Switzerland

2. Department of Plant Pathology, University of Wisconsin-Madison , Madison , WI 53706 , USA

3. Wisconsin Institute for Discovery , Madison , WI 53706 , USA

4. Systematic Biology, Department of Organismal Biology, Uppsala University , Uppsala , 752 36 , Sweden

Abstract

Abstract Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships are giant fungal CMEs whose functions are largely unknown because they require time-intensive manual curation. To address this knowledge gap, we developed starfish, a computational workflow for high-throughput eukaryotic CME annotation. We applied starfish to 2 899 genomes of 1 649 fungal species and found that starfish recovers known Starships with 95% combined precision and recall while expanding the number of annotated elements ten-fold. Extant Starship diversity is partitioned into 11 families that differ in their enrichment patterns across fungal classes. Starship cargo changes rapidly such that elements from the same family differ substantially in their functional repertoires, which are predicted to contribute to diverse biological processes such as metabolism. Many elements have convergently evolved to insert into 5S rDNA and AT-rich sequence while others integrate into random locations, revealing both specialist and generalist strategies for persistence. Our work establishes a framework for advancing mobile element biology and provides the means to investigate an emerging dimension of eukaryotic genetic diversity, that of genomes within genomes.

Funder

Wisconsin Alumni Research Foundation

University of Wisconsin-Madison

European Union's Horizon 2020

Marie Skłodowska-Curie

Swedish Research Council Formas

Swedish Research Council VR

Publisher

Oxford University Press (OUP)

Reference94 articles.

1. Transposable elements;Hayward;Curr. Biol.,2022

2. Introduction: the secret lives of microbial mobile genetic elements;Hall;Philos. Trans. R. Soc. B Biol. Sci.,2022

3. A devil's bargain with transposable elements in plant pathogens;Fouché;Trends Genet.,2021

4. Paleovirology of the DNA viruses of eukaryotes;Barreat;Trends Microbiol.,2022

5. The important contribution of transposable elements to phenotypic variation and evolution;Catlin;Curr. Opin. Plant Biol.,2022

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