Abstract
Transposable element (TE) expansion has long been known to mediate genome evolution and phenotypic diversity in organisms, but its impact on the evolution of posttranscriptional regulation following species divergence remains unclear. To address this issue, we performed long-read direct RNA sequencing, polysome profiling sequencing, and small RNA sequencing in the cotton genus Gossypium, the species of which range more than 3-fold in genome size. We found that TE expansion contributed to the turnover of transcription splicing sites and regulatory sequences, leading to changes in alternative splicing patterns and the expression levels of orthologous genes. We also found that TE-derived uORFs (upstream open reading frames) and microRNAs (miRNAs) served as regulatory elements mediating differences in the translation levels of orthologous genes. We further identified genes that exhibited lineage-specific divergence at the transcriptional (5,694 genes), splicing (5,255 genes) and translational (5,570 genes) levels, and showcased the high flexibility and fluidity of gene expression regulation in the evolutionary process. Our work highlights the significant role of TE in driving posttranscriptional regulation divergence in the cotton genus, and offers insights for deciphering the evolutionary mechanisms of cotton species and the formation of biological diversity.