Long-read genome assembly of the insect model organism Tribolium castaneum reveals extensive propagation of satellite DNA long arrays in gene-rich regions

Abstract

Eukaryotic genomes are replete with satellite DNAs (satDNAs), large stretches of tandemly repeated sequences which are mostly underrepresented in genome assemblies. Here we combined Nanopore long-read sequencing with a reference-guided assembly approach, to generate an improved, high-quality genome assembly TcasONT of the model beetle Tribolium castaneum. Enriched by 45 Mb in the repetitive part, the new assembly comprises almost the entire genome sequence. We used the enhanced assembly to conduct global and in-depth analyses of abundant euchromatic satDNAs, Cast1-Cast9. Contrary to the commonly adopted view, our finding showed the extensive spread of satDNAs in gene-rich regions, including long arrays. The results of the principal component analysis of monomers and sequence similarity relationships between satDNA arrays, revealed an occurrence of recent satDNAs array exchange between different chromosomes. We proposed a scenario of their genome dynamics characterized by repeated bursts of satDNAs spreading through euchromatin, followed by a process of elongation and homogenization of arrays. We also found that suppressed recombination on the X chromosome has no significant effect on the spread of satDNAs, but rather tolerates the amplification of these satDNAs into longer arrays. Analyses of arrays neighboring regions showed a tendency of one Cast satDNA to be associated with transposon-like elements. Using 2D electrophoresis followed by Southern blotting, we proved Cast satDNAs presence in the fraction of extrachromosomal circular DNA (eccDNA). We point to two mechanisms that enable the said satDNA spread to occur: transposition by transposable elements and insertion mediated by eccDNA. The presence of such a large proportion of satDNA in gene-rich regions inevitably gives rise to speculation about their possible influence on gene expression.