Comparative genomic and transcriptome analyses of transposable elements in buffalo identify key short interspersed element-derived genes for testicular and muscle development.

Transposable elements (TE) are widespread genetic components that affect the structure and function of eukaryotic genomes. However, the comprehensive genomic and transcriptome characterization of buffalo TE remains unclear. Here, we first constructed a pan-TE library from 7 buffalo genomes representing both river and swamp buffalo breeds. We identified 46,389 unique TE comprising 15,975 cores and 30,414 variable elements. These TE span approximately 1.04 Gb and its length account for 33.53% of the buffalo reference genome. The core TE exhibited distinct chromosomal patterns, with the long-interspersed element (LINE), short interspersed element (SINE), and long-terminal repeats (LTR) superfamilies representing the most abundant groups, which varied across subspecies and individuals. Notably, these elements showed a preference for genic regions, with DNA and LTR transposons frequently located within gene introns. Transcriptomic analysis revealed that the TE-derived genes displayed tissue-specific expression, particularly in somatic and gametic tissues. Co-expression analysis identified several SINE-derived hub genes that played key roles in testicular and muscle tissue development. This study provides a comprehensive buffalo pan-TE library, offering an invaluable resource for exploring TE functions, and laying the foundation for future transposome studies in buffalo genetics.