rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences

Abstract In this study, we introduce a novel approach for analysing long, repetitive genomic sequences. Our methods significantly advance research on rDNA polymorphism. First, we describe a technique for isolating high-molecular-weight DNA from individual chromosomes, enabling selective enrichment of sequencing libraries for extensive genomic regions of interest. Second, we present rDNAmine, a bioinformatic toolkit for capturing and examining large repetitive arrays in Oxford Nanopore sequencing data. This approach facilitates the study of polymorphisms within long repeats, bypassing traditional alignment-based methods and providing a more efficient and scalable solution for investigating repetitive regions. We demonstrate the effectiveness of our approach through the analysis of rDNA arrays in two yeast species, Saccharomyces cerevisiae and Candida albicans. In S. cerevisiae, rDNA arrays show limited polymorphism, while in C. albicans, we observe substantial variation in rDNA module size, with two distinct repeat populations within the array. These findings reveal species-specific differences in the structural organisation of rDNA loci, highlighting the diverse nature of tandem repeat architecture. The rDNAmine toolkit is broadly applicable to various organisms and repetitive genomic contexts, offering a versatile platform for studying repetitive sequences. Take Away Yeast rDNA serves as a benchmark to validate tools for analysing long repetitive sequences. A chromosome-specific DNA extraction method has been introduced to enable targeted enrichment of repetitive loci. The rDNAmine pipeline was designed to analyse long tandem repeats from noisy long-read data without requiring global alignment. Competing Interest Statement The authors have declared no competing interest.