Abstract
Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading to TE propagation. Recent studies in yeast did not find any increase in transposition rate in hybrids. However, this does not rule out the possibility that the transcriptional or translational activity of TEs increases following hybridization because of a disruption of the host TE control mechanisms. Thus, whether total expression of a TE family is higher in hybrids than in their parental species remains to be examined. We leveraged publically available RNA-seq and ribosomal profiling data on yeast artificial hybrids of the Saccharomyces genus and performed differential expression analysis of their LTR retrotransposons (Ty elements). Our analyses of total mRNA levels show that Ty elements are generally not differentially expressed in hybrids, even when the hybrids are exposed to a low temperature stress condition. Overall, only 2/26 Ty families show significantly higher expression in the S. cerevisiae × S. uvarum hybrids while there are 3/26 showing significantly lower expression in the S. cerevisiae x S. paradoxus hybrids. Our analysis of ribosome profiling data of S. cerevisiae × S. paradoxus hybrids shows similar translation efficiency of Ty in both parents and hybrids, except for Ty1_cer showing higher translation efficiency. Overall, our results do not support the hypothesis that hybridization could act as a systematic trigger of TE expression in yeast and suggest that the impact of hybridization on TE activity is strain and TE specific.
Highlights
Genome diversification resulting from interspecific hybridization allows the development of novel phenotypes, creating an adaptive potential that can empower hybrids to colonize new niches (Runemark et al, 2019; Steensels et al, 2021)
Since we select for A nucleotides at the 3′ end of RNA sequencing (RNA-seq) reads, homopolymers of A in the reference sequences could be associated with higher mapping, for instance because of library contamination by fragments that would not correspond to the 3′ portion of transcripts
For DS2 and DS3, the coverage is fairly uniform along the sequence, as expected from mRNA sequencing with a single poly-A selection (Figure 2B, Supplementary Figure 1)
Summary
Genome diversification resulting from interspecific hybridization allows the development of novel phenotypes, creating an adaptive potential that can empower hybrids to colonize new niches (Runemark et al, 2019; Steensels et al, 2021). TEs are dispersed repeated sequences that can propagate within a genome (Bourque et al, 2018). They are ubiquitous in eukaryotes but represent various genome proportions in different species. TEs generate genomic insertions that are mostly selectively neutral or slightly deleterious (Doolittle and Sapienza, 1980). Because of their detrimental effects, TEs are often compared to parasites spreading selfishly within their host genome (Orgel and Crick, 1980). One source of deleteriousness of TE multiplication is the resulting increase in genome size and complexity, which can lead to increased instability and to phenotypic changes (Kidwell and Lisch, 1997). TE mobilization is likely to reduce the fitness of the host
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