Exploring nanopore long reads and whole-genome sequencing data to characterize long tandem repeats and chromosome structure in mammalian genomes

Abstract

Long tandem repeats (LTRs) sequences, namely satellite DNA (satDNA), play a critical role in genome organization and stability. Their detection and characterization still represent a challenge, which long-read Nanopore sequencing is helping to simplify. Thus, there is a growing interest in developing bioinformatic tools for the analysis of LTRs and in understanding their role in genome evolution. The main aim of this work was the characterization of LTRs in mammalian genomes, using WGS data from two model organisms: Peromyscus genus and Homo sapiens. In the first case, the focus was to characterize PMSat, an evolutionarily conserved satDNA. In the second case, the key objective was to perform a comparative assessment of LTRs between different human long-read genome datasets, to characterize in detail the human satellite HSat1A and its transcripts, and to establish methods to analyze satDNA involvement in Robertsonian translocations (specifically the t(14;21)). The analysis performed identified PMSat as the most abundant LTR of the Peromyscus genus, in accordance with previous cytogenetic studies, with GC-content, monomer and array length exhibiting little variation. Moreover, a tendency in the positioning in Peromyscus genus chromosomes was identified. In the study of the three WGS Nanopore human datasets, the LTRs ALR, BSR, HSat2 and HSat1A were identified as the most abundant. It was possible to demonstrate the potential of chromosome sorting to facilitate the analysis of translocated chromosomes. However, low sequencing yield and DNA fragmentation did not allow for characterization of the target region. Finally, LTRs of HSat1A were shown to have a predominance of 9-mer monomers, and to express polyadenylated transcripts of varying lengths, probably resulting from alternative polyadenylation. This study represents a relevant contribution to understanding the role of LTRs in genome organization and evolution.