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The satellitome of the confused flour beetle Tribolium confusum: genomic and cytogenetic aspects

The confused flour beetle Tribolium confusum is a major stored products pest which is spread worldwide. It is also present in laboratory research as it is an excellent model for population and genetic studies. The genome of the beetle T. confusum contains large blocks of heterochromatin, which makes it suitable for studying non-coding DNA sequences. The most intriguing class of non- coding DNAs are satellite DNAs (satDNAs), tandemly repeated sequences primarily associated with the centromeric and telomeric parts of eukaryotic chromosomes. One major satDNA family dominates the genome of the confused flour beetle amounting to the total of 40% of its genomic sequence. The aim of this work was to investigate whether there are other satellite DNAs in the genome of T. confusum besides the major satDNA family. Using two different types of high-throughput sequencing on the Illumina and PacBio platforms and the bioinformatic pipeline TAREAN, we characterized for the first time 16 new satDNAs in the genome of T. confusum defining its satellitome. Considering their abundance, and compared to the major satDNA, which is a high-copy-number satellite, two newly discovered satDNAs are categorized as moderate-copy and the remaining 14 as low-copy-number satellites. Chromosomal location and organization of the satDNA representatives for each group were determined by fluorescence in situ hybridization (FISH) on metaphase chromosome spreads (2n=18) and on the extended DNA fibers. The different distribution patterns of the studied satDNAs correspond to their genomic abundance, with low-copy-number satellites being chromosome-specific. We found that one of the chromosome-specific low-copy-number satellites is also present in the genomes of other Tribolium species, specifically T. castaneum, T. freemani and T. madens. By exploring the different satDNA families that make up the genome of T. confusum, we are getting closer to understanding the genome of this important pest, but also to understanding the evolution of satDNAs within the genus Tribolium.

Tribolium confusum ; satellitome ; whole genome sequencing ; cytogenetics

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