Transposable element persistence via potential genome-level ecosystem engineering

• Published in: BMC genomics Vol. 21; no. 1; p. 367
• Main Authors: Kremer, Stefan C, Linquist, Stefan, Saylor, Brent, Elliott, Tyler A, Gregory, T Ryan, Cottenie, Karl
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 19.05.2020; BioMed Central; BMC
• Subjects: Accumulation; Analysis; Asexuality; Biological Coevolution; C-value paradox; Computer simulation; Density; Deoxyribonucleic acid; DNA; DNA Transposable Elements - genetics; DNA Transposable Elements - physiology; Ecological conditions; Ecological effects; Ecosystem; Ecosystem engineering; Ecosystems; Environmental changes; Eukaryota - genetics; Eukaryotes; Evolution, Molecular; Gene sequencing; Genetic Fitness; Genome; Genome-level ecology; Genomes; Genomic Instability; Genomics; Junk DNA; Models, Genetic; Mutation; Parasites; Population; Replication; Transposon accumulation; Transposon ecology; Transposons; Transposon ecology; Ecosystem engineering; C-value paradox; Genome-level ecology; Junk DNA; Transposon accumulation
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6763-1

The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE accumulation remain poorly understood. Most previous attempts to identify these conditions have focused on evolutionary processes occurring at the host organism level, whereas we explore a TE ecology explanation. As an alternative (or additional) hypothesis, we propose that ecological mechanisms occurring within the host cell may contribute to patterns of TE accumulation. To test this idea, we conducted a series of experiments using a simulated asexual TE/host system. Each experiment tracked the accumulation rate for a given type of TE within a particular host genome. TEs in this system had a net deleterious effect on host fitness, which did not change over the course of experiments. As one might expect, in the majority of experiments TEs were either purged from the genome or drove the host population to extinction. However, in an intriguing handful of cases, TEs co-existed with hosts and accumulated to very large numbers. This tended to occur when TEs achieved a stable density relative to non-TE sequences in the genome (as opposed to reaching any particular absolute number). In our model, the only way to maintain a stable density was for TEs to generate new, inactive copies at a rate that balanced with the production of active (replicating) copies. From a TE ecology perspective, we suggest this could be interpreted as a case of ecosystem engineering within the genome, where TEs persist by creating their own "habitat".