Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Hybridization can induce transposons to jump into new genomic positions,
which may result in their accumulation across the genome. Alternatively,
transposon copy numbers may increase through non-allelic (ectopic)
homologous recombination in highly repetitive regions of the genome. The
relative contribution of transposition bursts versus recombination-based
mechanisms to evolutionary processes remains unclear because studies on
transposon dynamics in natural systems are rare. We assessed the
genome-wide distribution of transposon insertions in a young hybrid
lineage (“invasive Cottus”, n=11) and its parental species Cottus rhenanus
(n=17) and Cottus perifretum (n=9) using a reference genome assembled from
long single molecule PacBio reads. An inventory of transposable elements
was reconstructed from the same data and annotated. Transposon copy
numbers in the hybrid lineage increased in 120 (15.9%) out of 757
transposons studied here. The copy number increased on average by 69%
(range: 10 – 197 %). Given the age of the hybrid lineage, this suggests
that they have proliferated within a few hundred generations since
admixture began. However, frequency spectra of transposon insertions
revealed no increase of novel and rare insertions across assembled parts
of the genome. This implies that transposons were added to repetitive
regions of the genome that remain difficult to assemble. Future studies
will need to evaluate whether recombination-based mechanisms rather than
genome-wide transposition may explain the majority of the recent
transposon proliferation in the hybrid lineage. Irrespectively of the
underlying mechanism, the observed over-abundance in repetitive parts of
the genome suggests that gene-rich regions are unlikely to be directly
affected.