A Deep Dive into Allium Satellite DNAs: Expansion and Characterization of the <i>Allium cepa</i> and <i>Allium fistulosum</i> Satellitomes

Satellite DNA (satDNA) is a family of tandemly repeated non-coding sequences in eukaryotic genomes involved in shaping genome architecture and regulation of various biological functions. Within a species, all satDNA families collectively form the satellitome. Satellitomes of Allium species has been explored only superficially, largely due to enormous genome sizes, high transposable element content, and a general lack of reference genomic resources. The emergence of reference genome assemblies now makes it possible to conduct a more in-depth study. Here, we applied a comprehensive bioinformatics approach to study the satellitomes of <i>Allium cepa</i> and <i>Allium fistulosum</i>. Using two complementary bioinformatics pipelines along with available reference genome assemblies, we have created the most complete collection of consensus satDNA sequences of <i>A. cepa</i> and <i>A. fistulosum</i> so far, consisting of 83 and 97 consensus sequences, respectively. The <i>in silico</i> analysis of the genomic distribution allowed the identification of 11 novel candidates for cytogenetic marker panels, including chromosome-specific satDNA families. Validation of satDNA using PCR and FISH confirmed the reliability of the created satellitomes. Furthermore, comparative analysis of satDNA genomic organization and abundance provided insights into the evolution of these species satellitomes. These findings provide a foundational resource that will help illuminate the evolutionary dynamics of Allium satellitomes and pave the way for future cytogenetic studies of Allium species.