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Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant  Senna tora  dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the  S. tora  genome and compared the chromosomal distribution of these repeats between  S. tora  and a closely related euploid,  Senna occidentalis . Using a read clustering algorithm, we identified the major  S. tora  tandem repeats and visualized their chromosomal distribution by fluorescence  in situ  hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the  S. tora  genome. The unit lengths and copy numbers had ranges of 7–5,833 bp and 325–2.89 × 10 6 , respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG) n  was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in  Senna occidentalis , was predominantly pericentromeric in  S. tora . The unusual chromosomal distribution of tandem repeats in  S. tora  not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.

Chromosomal Mapping of Tandem Repeats Revealed Massive Chromosomal Rearrangements and Insights Into Senna tora Dysploidy