engleski

Satellitome analysis of the black flour beetle Tribolium madens

Satellite DNA (satDNA) sequences have for long been underrepresented in the genomic studies, primarily due to their non-coding nature and repetitive organization in a genome. Nevertheless, with the advances in third-generation sequencing technologies and tailored bioinformatic tools, it has become possible to characterise a large number of satDNA families in the genomes. Therefore, the term satellitome has been introduced to signify a collection of all satDNA families in one species. Species of the genus Tribolium are known to have a high content of satDNAs in their genomes. The black flour beetle Tribolium madens has two major satDNAs characterised, together comprising one third of the genome. The aim of this research was to characterise the T. madens satellitome comprehensively by discovering hitherto unknown low-copy satDNAs in order to unmask the setup of tandemly repeated sequences in the genome of this species. To achieve this goal, we sequenced the T. madens genome using two different high-throughput sequencing technologies. Using Illumina platform, 151 bp short reads were obtained and analysed by the computer pipeline TAREAN which defined low- copy satDNAs and their consensus sequences. Sequencing by PacBio HiFi technology generated 15- kb-long, highly accurate reads which were used to study the genomic organisation of the newly defined satDNAs. By this approach, over 100 new satDNAs in the genome of T. madens were defined, while 10 of the most prominent satDNA families were further characterised experimentally. Fluorescence in situ hybridisation revealed that the newly detected satDNAs are scattered throughout the genome, not present on all the chromosomes of the complement (2n = 20 + supernumerary chromosomes). Orthologous sequences of the T. madens low-copy satDNAs were disclosed in the genomes of related species Tribolium castaneum and Tribolium freemani, revealing that some of the satDNAs in the genus Tribolium evolve according to the concept of concerted evolution. Although still underestimated in relation to coding DNA studies, comparative satellitome analyses advance our understanding of the genome divergence between closely related species and may provide valuable insights into their evolution and speciation.

satellitome ; Tribolium madens

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