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Background  The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus  Trematomus  (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity. Here we apply a multi-strategy approach to determine the role of large-scale TE mobilization in chromosomal diversification within  Trematomus  species.    Results  Despite the extensive chromosomal rearrangements observed in  Trematomus  species, our measurements revealed strong interspecific genome size conservation. After identifying the  DIRS1 ,  Gypsy  and  Copia  retrotransposon superfamilies in genomes of 13 nototheniid species, we evaluated their diversity, abundance (copy numbers) and chromosomal distribution. Four families of  DIRS1 , nine of  Gypsy , and two of  Copia  were highly conserved in these genomes;  DIRS1  being the most represented within  Trematomus  genomes. Fluorescence in situ hybridization mapping showed preferential accumulation of  DIRS1  in centromeric and pericentromeric regions, both in  Trematomus  and other nototheniid species, but not in outgroups: species of the Sub-Antarctic notothenioid families Bovichtidae and Eleginopsidae, and the non-notothenioid family Percidae.    Conclusions  In contrast to the outgroups, High-Antarctic notothenioid species, including the genus  Trematomus , were subjected to strong environmental stresses involving repeated bouts of warming above the freezing point of seawater and cooling to sub-zero temperatures on the Antarctic continental shelf during the past 40 millions of years  (My) . As a consequence of these repetitive environmental changes, including thermal shocks; a breakdown of epigenetic regulation that normally represses TE activity may have led to sequential waves of TE activation within their genomes. The predominance of  DIRS1  in  Trematomus  species, their transposition mechanism, and their strategic location in “hot spots” of insertion on chromosomes are likely to have facilitated nonhomologous recombination, thereby increasing genomic rearrangements. The resulting centric and tandem fusions and fissions would favor the rapid lineage diversification, characteristic of the nototheniid adaptive radiation.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4714-x) contains supplementary material, which is available to authorized users.

Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: the case for the Antarctic teleost genus Trematomus