Abstract
Transposable elements (TEs) play important roles in physiological processes, but their function in tail development remains poorly characterized. To explore their potential regulatory roles, we systematically analyzed the expression patterns of TEs during different fetal developmental stages of the sheep tail. Using RNA-seq data and the TEtranscripts pipeline, we identified differentially expressed TEs. Our key findings are as follows: (i) SINE/MIR, L1, and BovB elements exhibited significant stage-specific expression. (ii) The number of differentially expressed TEs was dynamic, with 2129 identified between stages E40-45 and E55-60, and 5554 between E55-60 and E70-75. (iii) These TEs were primarily located in intergenic regions, introns, and 3'UTRs, and their expression trends were highly consistent with those of adjacent differentially expressed genes. (iv) Pathway enrichment analysis revealed that TEs and their correlated genes between E40-45 and E55-60 were predominantly involved in tail elongation, while the comparison between E55-60 and E70-75 highlighted pathways related to tail fat formation. Furthermore, we identified specific candidate TEs associated with vertebra formation and fat deposition. This study provides novel insights into the role of TEs in shaping tail phenotypes and offers valuable information for sheep breeding programs.