Title | Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. |
Publication Type | Journal Article |
Year of Publication | 2019 |
Authors | Dennenmoser, S, Sedlazeck, FJ, Schatz, MC, Altmüller, J, Zytnicki, M, Nolte, AW |
Journal | Mol Ecol |
Volume | 28 |
Issue | 6 |
Pagination | 1491-1505 |
Date Published | 2019 Mar |
ISSN | 1365-294X |
Keywords | Animals, DNA Copy Number Variations, DNA Transposable Elements, Evolution, Molecular, Fishes, Genome, Hybridization, Genetic |
Abstract | 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 nonallelic (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 genomewide 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 in 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 genomewide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed overabundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected. |
DOI | 10.1111/mec.14969 |
Alternate Journal | Mol Ecol |
PubMed ID | 30520198 |
Grant List | UM1-HG008898 / / UM1-HG008898 / International StGr EVOLMAPPING / / FP7 Ideas: European Research Council / International |
Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish.
Similar Publications
FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform. 2024;25(3). | .
Core planar cell polarity genes and in predisposition to congenital vertebral malformations. Proc Natl Acad Sci U S A. 2024;121(18):e2310283121. | .
NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy. Genome Med. 2024;16(1):53. | .