Asymmetric evolution of satellite DNA on homologous and homeologous chromosomes in allotetraploid Narenga porphyrocoma

Satellite DNA is a fundamental component of eukaryotic genomes, playing critical roles in chromosome organization and genome stability. Nevertheless, its evolutionary dynamics in allopolyploid plants remain poorly understood, primarily due to their inherent genomic complexity. Narenga porphyrocoma, an allotetraploid species within the Saccharum complex, possesses a distinctive karyotype consisting of 10 ancestral chromosomes and five derived chromosomes resulting from ancestral fusion events. This unique chromosomal configuration provides an exceptional model system for investigating the composition and evolutionary dynamics of satellite DNAs in an allotetraploid, particularly in the context of homologous and homeologous chromosomes within and between its two subgenomes. Here, we performed a genome-wide identification of satellite DNAs in the allotetraploid N. porphyrocoma GD35 by conducting sequence similarity-based clustering of low-coverage Illumina sequencing data. We identified six major satellite DNAs (NpSat1–NpSat6), which varied in their genomic abundance, monomer length, and GC content. Fluorescence in situ hybridization (FISH) revealed that NpSat1 localizes to the centromeric regions of all chromosomes, whereas the remaining five satellite DNAs exhibit subtelomeric distributions. Notably, three subtelomeric satellites (NpSat2, NpSat3, and NpSat5) with high sequence similarity were co-localized, occupying one or both ends of the majority of chromosomes. In contrast, NpSat4 and NpSat6 displayed restricted distribution patterns, with NpSat4 localizing to only 11 out of the 30 chromosome ends and NpSat6 being confined to just 2 specific chromosome ends. Strikingly, oligo-FISH analyses revealed the asymmetric distribution of these subtelomeric satellites not only between homologous chromosomes within the same subgenome but also between homeologous chromosomes across the two subgenomes. Comparative genomic and cytogenetic analyses further indicated that NpSat1 is evolutionarily conserved across the Saccharum complex, while the subtelomeric satellites exhibit species-specific distribution patterns or are exclusively shared with its close relative Erianthus rockii. Moreover, we developed a species-specific molecular marker based on NpSat6 that successfully authenticated intergeneric hybrids between sugarcane and N. porphyrocoma, confirming its practical utility in sugarcane breeding programs. In summary, our study establishes a cytogenetic framework for understanding the evolutionary patterns of satellite DNAs in N. porphyrocoma. Furthermore, the development of a satellite DNA-based molecular marker offers significant potential for hybrid identification in sugarcane breeding.