Transposable element landscapes provide insights into TE’s evolutionary convergence driven by asymmetric subgenome dynamics following allopolyploidization in cotton

Transposable elements (TEs) constitute the largest fraction of cotton genomes, serving as primary drivers for genome expansion and species diversification. However, comprehensive chromosomal physical maps visualizing the evolutionary dynamics of TEs between allotetraploid cotton (including naturally colored and white cotton) and related diploid progenitors remain scarce. Here, we reconstructed TE landscapes by integrating a de novo assembly approach with fluorescence in situ hybridization (FISH). Comparative FISH analysis of 31 distinct TEs revealed conserved chromosomal distribution patterns across naturally colored and white cotton cultivars, with the A-subgenome exhibiting significantly higher TEs abundance and diversity than the D -subgenome. Cytological analysis between diploid progenitor and allotetraploid cotton showed that most TEs (22/31) maintained conserved evolutionary patterns post-polyploidization, while only 9 TEs underwent marked abundance shifts. Notably, cytological and genomic analyses revealed eight unique TEs that were highly abundant in the A-diploid progenitor but either absent (six TEs) or present at extremely low levels (two TEs) in the D -diploid progenitor, however, following allopolyploidization, these TEs underwent massive amplification in the D -subgenome, even producing distinct FISH signals in the interstitial regions of all D -subgenome chromosomes. This leads us to hypothesize that asymmetric TE composition between A and D -subgenomes probably activates two complementary mechanisms—expansion of pre-existing D -subgenome TEs and invasion-driven amplification from the A-subgenome—collectively driving convergent evolution of the D subgenome toward an A-subgenome-like TE pattern, thereby potentially enhancing allotetraploid cotton genome stability. These findings provide further insights into the roles of TEs in cotton allopolyploidization and genome evolution from a cytological perspective. • Constructed comprehensive chromosomal TE landscapes for allotetraploid and diploid cottons using de novo assembly and FISH. • Revealed conserved TE patterns in colored/white allotetraploids, with A-subgenome showing higher abundance and diversity than D -subgenome. • Uncovered evolutionary dynamics of 31 TEs from diploid ancestors to allotetraploid cotton genomes. • Identified eight unique TEs massively expanding in D -subgenome post-polyploidization despite low ancestral levels. • Proposed asymmetric TE content drives D -subgenome TE convergent evolution toward A-like TE patterns via D expansion and A to D invasion.