Mravinac, B. | bioRxiv Science

bioRxiv2024

Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species

Tandemly repeated satellite DNAs (satDNAs) are among the most abundant and fastest-evolving eukaryotic sequences, but the way they model genomes is still elusive. Here, we investigated the evolutionary dynamics of satDNAs in the extremely satDNA-rich genomes of two closely related Tribolium insects that produce sterile hybrids. In Tribolium freemani, we identified 135 satDNAs, accounting for 38.7% of the genome. Comparative analysis with the Tribolium castaneum satellitome revealed that the drastic difference happened in their centromeric regions, which share orthologous organization hallmarked by totally different major satDNAs but related minor satDNAs. The T. freemani male sex chromosome, which lacks the major satDNA but contains a minor-like satDNA, further heightened the question of which satDNA is centromere-competent. By analyzing the long-range organization of the centromeric regions, we revealed that both the major and minor satDNA arrays exhibit a strong tendency toward macro-dyad symmetry, suggesting that the secondary structures in the centromeres may be more important than the primary sequence itself. We found evidence that the centromeric satDNAs of T. freemani occur in extrachromosomal circular DNAs, which may contribute to their expansion and homogenization between non-homologous chromosomes. We also identified numerous low-copy-number satDNAs that are orthologous between the siblings, some of which are associated with transposable elements, highlighting transposition as a mechanism of their spreading. The dynamic evolution of satDNAs has clearly influenced the differentiation of Tribolium genomes, but the question remains whether the differences in their satDNA profiles are a cause or consequence of speciation.

genomics↗

bioRxiv2023

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

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.

genomics↗