SatXplor-a comprehensive pipeline for satellite DNA analyses in complex genome assemblies

Area of Science:

• Genomics
• Bioinformatics
• Molecular Evolution

Background:

• Satellite DNAs (satDNAs) are abundant repetitive sequences crucial for genome organization and evolution.
• satDNAs are often underrepresented in genome assemblies, hindering comprehensive analysis.
• Existing tools struggle with the complexity and repetitive nature of satDNAs.

Purpose of the Study:

• To introduce SatXplor, a novel computational pipeline for robust characterization of satDNA elements.
• To enable detailed analysis of satDNA arrays and their flanking genomic regions.
• To provide a versatile tool for exploring satDNA organization, variation, and evolutionary aspects.

Main Methods:

• Development of a novel bioinformatics pipeline, SatXplor.
• Benchmarking SatXplor against existing tools and curated datasets from diverse species (e.g., mice, humans).
• Integration of sequence analysis, homology investigation, clustering, and graph-based methods.

Main Results:

• SatXplor demonstrates versatility across genomes with varying complexities and satDNA profiles.
• The pipeline accurately identifies tandemly repeated sequences and annotates satDNA arrays.
• SatXplor enables novel evaluation of satDNA variation and its surrounding genomic landscape.

Conclusions:

• SatXplor offers a comprehensive and innovative approach to satDNA analysis.
• The tool provides crucial insights into the structural characteristics and genomic context of satDNA elements.
• SatXplor facilitates a deeper understanding of satDNA organization and evolutionary mechanisms.