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Satellitome characterization of the black flour beetle Tribolium madens

Heterochromatic regions of eukaryotic genomes consist of large portions of repetitive DNA elements. Repetitive DNA elements are often dominated by satellite DNAs (satDNAs), tandemly repeated non-coding sequences located primarily in the (peri)centromeric and (sub)telomeric chromosomal regions [1]. Although detecting these sequences in a genome used to be difficult, high-throughput sequencing technologies now allow the disclosure of entire satellitomes, i.e., comprehensive collections of satDNAs in a single genome. The black flour beetle Tribolium madens belongs to the genus Tribolium, whose species are known for a large share of satDNAs in the genome content. So far, the two satDNAs have been detected in T. madens, comprising together 34% of the genomic DNA [2]. However, there is no evidence as yet of other T. madens satDNAs. In this work, we addressed the T. madens satellitome by applying high-throughput sequencing approach. First, we sequenced the whole T. madens genome by two different technologies - NGS based on sequencing by synthesis performed by Illumina and single-molecule, real-time sequencing performed by PacBio. Based on the unassembled short Illumina reads, the computational pipeline TAREAN [3] defined the putative satDNA consensus repeat units. By mapping the consensus sequences to the long and highly accurate PacBio HiFi reads we explored their tandem organization. In this way we discovered ten new satDNAs. As each of newly detected satDNA comprises less than 0.05% of the genome, these sequences represent low copy satDNAs. Fluorescence in situ hybridization revealed that the low-copy satDNAs are scattered on different chromosomes of the complement (2n=20 + supernumerary chromosomes). To gain insight into the evolution of T. madens satDNAs, we further investigated whether there were similar sequences in the genomes of closely related species Tribolium castaneum and Tribolium freemani. The satDNAs, which have the orthologous sequences in the related genomes, have been shown to evolve according to the principles of concerted evolution. Comparative analyses of the satellitomes of the congeneric species not only illuminate the evolution of repetitive sequences, but also might further our understanding of the genetic differences that could lead to speciation.

Satellitome ; Tribolium madens ; WGS

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