engleski

Low-copy satellite DNAs of the flour beetle Tribolium castaneum revealed by next generation sequencing

Satellite DNAs (satDNAs) are tandemly repeated sequences prevalent in (peri)centromeric chromosomal regions that represent one of the most enigmatic parts of eukaryotic genomes. The red flour beetle Tribolium castaneum is an excellent model organism used in molecular studies for decades. Ten years ago its genome was sequenced by a shotgun approach ; however, 20% of the genome is omitted from the current assembly due to the repetitive setup based primarily on satDNAs. In course of the study of centromeric DNA sequences in T. castaneum, we re-sequenced its genome by Illumina Next-Generation Sequencing (NGS). The satellitome, representing the complete set of satDNAs in the genome, was analyzed by a computational pipeline TAREAN, which enables detection of putative satellite sequences from unassembled short reads. We identified three novel T. castaneum satDNAs that have not been detected in the previous studies. In spite of low contribution to the genome (<0.1%), we successfully proved tandem organisation of these repeats by Southern blot method. Fluorescence in situ hybridization also revealed their localization on different chromosomal subsets. By combining bioinformatics tools and experimental procedures we affirmed the applicability of NGS unassembled reads in detection and characterization of low-copy satDNAs, which might be relevant to understanding genome structure and function.

satellite DNA ; Tribolium castaneum ; satellitome ; Next-Generation Sequencing

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